Re: [gmx-users] after using ACPYPE , GROMACS OPLS itp file generated an atom type like opls_x with mass 0.000
Hi, this feature is really really experimental and should indeed be avoided. If opls you want, then give a try with http://www.aribeiro.net.br/mktop/ Alan On 8 November 2013 04:42, aditya sarma adityasrm...@gmail.com wrote: Hi, i was trying to generate topology for p-phenylene vinylene polymer for OPLS forcefield using acpype . The itp file i got has the atomtype opls_x with mass 0.00. Is there any way to rectify this? After reading through how acpype works i found out this was one of the possible errors but there was no solution to it. This is a part of the itp file generated: [ atoms ] ; nr type resi res atom cgnr charge mass ; qtot bond_type 1 opls_145 1 LIG C1-0.117500 12.01100 ; qtot -0.118 CA 2 opls_145 1 LIGC12-0.055800 12.01100 ; qtot -0.173 CA 3 opls_145 1 LIGC23-0.117500 12.01100 ; qtot -0.291 CA 4 opls_145 1 LIGC34-0.131000 12.01100 ; qtot -0.422 CA 5 opls_145 1 LIGC45-0.125000 12.01100 ; qtot -0.547 CA 6 opls_145 1 LIGC56-0.131000 12.01100 ; qtot -0.678 CA 7 opls_x 1 LIGC67-0.099200 0.0 ; qtot -0.777 x 8 opls_x 1 LIGC78-0.105200 0.0 ; qtot -0.882 x 9 opls_145 1 LIGC89-0.048800 12.01100 ; qtot -0.931 CA 10 opls_145 1 LIGC9 10-0.119500 12.01100 ; qtot -1.051 CA 11 opls_145 1 LIG C10 11-0.118500 12.01100 ; qtot -1.169 CA 12 opls_145 1 LIG C11 12-0.051800 12.01100 ; qtot -1.221 CA 13 opls_145 1 LIG C12 13-0.118500 12.01100 ; qtot -1.339 CA 14 opls_145 1 LIG C13 14-0.119500 12.01100 ; qtot -1.459 CA 15 opls_x 1 LIG C14 15-0.101200 0.0 ; qtot -1.560 x 16 opls_x 1 LIG C15 16-0.103200 0.0 ; qtot -1.663 x 17 opls_145 1 LIG C16 17-0.049800 12.01100 ; qtot -1.713 CA 18 opls_145 1 LIG C17 18-0.119500 12.01100 ; qtot -1.833 CA 19 opls_145 1 LIG C18 19-0.119000 12.01100 ; qtot -1.952 CA 20 opls_145 1 LIG C19 20-0.050800 12.01100 ; qtot -2.002 CA 21 opls_145 1 LIG C20 21-0.119000 12.01100 ; qtot -2.121 CA 22 opls_145 1 LIG C21 22-0.119500 12.01100 ; qtot -2.241 CA 23 opls_x 1 LIG C22 23-0.102200 0.0 ; qtot -2.343 x 24 opls_x 1 LIG C23 24-0.102200 0.0 ; qtot -2.445 x 25 opls_145 1 LIG C24 25-0.050800 12.01100 ; qtot -2.496 CA 26 opls_145 1 LIG C25 26-0.119000 12.01100 ; qtot -2.615 CA 27 opls_145 1 LIG C26 27-0.119000 12.01100 ; qtot -2.734 CA 28 opls_145 1 LIG C27 28-0.050800 12.01100 ; qtot -2.785 CA 29 opls_145 1 LIG C28 29-0.119000 12.01100 ; qtot -2.904 CA 30 opls_145 1 LIG C29 30-0.119000 12.01100 ; qtot -3.023 CA 31 opls_x 1 LIG C30 31-0.102200 0.0 ; qtot -3.125 x 32 opls_x 1 LIG C31 32-0.102200 0.0 ; qtot -3.227 x 33 opls_145 1 LIG C32 33-0.050800 12.01100 ; qtot -3.278 CA 34 opls_145 1 LIG C33 34-0.119000 12.01100 ; qtot -3.397 CA 35 opls_145 1 LIG C34 35-0.119000 12.01100 ; qtot -3.516 CA 36 opls_145 1 LIG C35 36-0.050800 12.01100 ; qtot -3.567 CA 37 opls_145 1 LIG C36 37-0.119000 12.01100 ; qtot -3.686 CA 38 opls_145 1 LIG C37 38-0.119000 12.01100 ; qtot -3.805 CA 39 opls_x 1 LIG C38 39-0.102200 0.0 ; qtot -3.907 x 40 opls_x 1 LIG C39 40-0.102200 0.0 ; qtot -4.009 x 41 opls_145 1 LIG C40 41-0.050800 12.01100 ; qtot -4.060 CA 42 opls_145 1 LIG C41 42-0.119000 12.01100 ; qtot -4.179 CA 43 opls_145 1 LIG C42 43-0.119500 12.01100 ; qtot -4.299 CA 44 opls_145 1 LIG C43 44-0.049800 12.01100 ; qtot -4.348 CA 45 opls_145 1 LIG C44 45-0.119500 12.01100 ; qtot -4.468 CA 46 opls_145 1 LIG C45 46-0.119000 12.01100 ; qtot -4.587 CA 47 opls_x 1 LIG C46 47-0.103200 0.0 ; qtot -4.690 x 48 opls_x 1 LIG C47 48-0.101200 0.0 ; qtot -4.791 x -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests
Re: [gmx-users] Ligand breaking in to two
Have you tested your ligand alone in MD simulation and how vmd would show it? Alan On 21 October 2013 08:31, MUSYOKA THOMMAS mutemibiochemis...@gmail.comwrote: Dear Users, I am doing protein-ligand MD simulations. I first prepare the ligand by adding Hydrogen atoms and setting the charges using UCSF chimera. I thereafter use acpype to get the ligand's gro,itp and top files. Finally, i process the protein.PDB file and perform MD simulations. However, when I combine the ligand and protein gro files and convert the resulting complex to a PDB file so as to visualise with VMD, the ligand always appears to be broken in two parts. Any advice on how to overcome this? Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 (0)1223 494588 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problem with the amb2gmx.pl
Hi, try ACPYPE. Alan On 9 October 2013 14:07, xiao helitr...@126.com wrote: Dear all, I am doing membrane protein simulation by using amber force field. The lipid force field parameters are from the lipid11.dat from Amber. Firstly, i got the xx.prmtop and xx.prmcrd files, and then i used amb2gmx.pl to convert the xx.prmtop and xx.prmcrd files into gromacs files xx.top and xx.gro files. However, i found there is some problem with the xx.top files. For example, there are two dihedral parameters, and they should be same, but in the xx.top file (gromacs form) ,they are different. I have no idea where the problem is from. Any information is appreciated! Fugui -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 (0)1223 494588 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Re: [gmx-users] problem with the amb2gmx.pl
And ACPYPE does (besides several others improvements) Alan On 9 October 2013 15:24, xiao helitr...@126.com wrote: Hi Alan, Thank you very much! The problem is solved. The reason is that amb2gmx cannot distinguish the proper and improper dihedrals. Best wishes Fugui At 2013-10-09 21:58:29,Alan alanwil...@gmail.com wrote: Hi, try ACPYPE. Alan On 9 October 2013 14:07, xiao helitr...@126.com wrote: Dear all, I am doing membrane protein simulation by using amber force field. The lipid force field parameters are from the lipid11.dat from Amber. Firstly, i got the xx.prmtop and xx.prmcrd files, and then i used amb2gmx.pl to convert the xx.prmtop and xx.prmcrd files into gromacs files xx.top and xx.gro files. However, i found there is some problem with the xx.top files. For example, there are two dihedral parameters, and they should be same, but in the xx.top file (gromacs form) ,they are different. I have no idea where the problem is from. Any information is appreciated! Fugui -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 (0)1223 494588 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 (0)1223 494588 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Ligand charge issues
In https://code.google.com/p/acpype/ you can look the wikis and you see the explanations about the partial charges. The best solution, though not straightforward, would be using http://q4md-forcefieldtools.org/REDS/ Alan On 2 September 2013 11:27, Muhammad Ayaz Anwar ayazan...@hotmail.comwrote: Hi Gromacs users, I am studying the protein-ligand interaction using amber99sb-ILDN force field in gromacs 4.6.2. To create the ligand topology (lipid A), I have used online version of ACPYPE/antechamber. http://webapps.ccpn.ac.uk/acpype/ I have read a lot more time that charge on different atoms are not correct when created through various softwares/scripts. My question is whether ACPYPE/antechamber also fall in this category? If yes, can anyone please provide me with any link from where I can get charge values to assign? Thank you.mayaz -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 (0)1223 494588 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Problem with Amber99SB-ILDN ff
Hi I can't see which commands you typed. Your second try /bin/sh: 1: -i: not found means that you $PATH is not properly setup for Amber Tools. And if you using open babel, it has to be your $PATH as well. For the first case, it's all about which structure you were trying to run. From the pdbs you sent me, none of them are correct. The test.pdb is not in a zwitterionic form and ACPYPE can only work with one residue only, so op-glu2.pdb is not OK either. Nevertheless, the error messages ACPYPE printed are re ANTECHAMBER, and once we cleared your structure, you'd better ask at AMBER list for this issues. But bear in mind that because ACPYPE is based on Antechamber, it will as well inherit some of its limitations like not being possible to work with organic molecule with open valences; containing others atoms than C, N, O, S, P, H, F, Cl, Br and I; or covalently bonded to another molecule. If one wants parameters for a modified amino acid residue, one way of getting it is by neutralising the N- and C- termini of the 2 adjacent residues (so make a tripeptide) and then fit manually the additional parameters to the modified residue. Alan On 17 July 2013 14:30, Melchor S. msm...@cid.csic.es wrote: Hi again, I can give more details about acpype error. This is the error that I obtained, === | ACPYPE: AnteChamber PYthon Parser interfacE v. 2012-09-13 14:55:47Z Rev: 389 (c) 2012 AWSdS | === == ... charge set to 0 == ... converting pdb input file to mol2 input file == * Babel OK * == Executing Antechamber... ++start_quote+++ Warning: the assigned bond types may be wrong, please : (1) double check the structure (the connectivity) and/or (2) adjust atom valence penalty parameters in APS.DAT, and/or (3) increase PSCUTOFF in define.h and recompile bondtype.c Be cautious, use a large value of PSCUTOFF (100) will significantly increase the computation time Running: /home/melchor/Software/amber12/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac Running: /home/melchor/Software/amber12/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff Total number of electrons: 61; net charge: 0 INFO: Number of electrons is odd: 61 Please check the total charge (-nc flag) and spin multiplicity (-m flag) Running: /home/melchor/Software/amber12/bin/sqm -O -i sqm.in -o sqm.out Error: cannot run /home/melchor/Software/amber12/bin/sqm -O -i sqm.in -o sqm.out of bcc() in charge.c properly, exit ++end_quote+ ERROR: Antechamber failed ++start_quote+++ /bin/sh: 1: -i: not found ++end_quote+ ERROR: Parmchk failed ERROR: Tleap failed == ... trying Sleap == Executing Sleap... ++start_quote+++ ++end_quote+ ++start_quote+++ /bin/sh: 1: -f: not found ++end_quote+ ERROR: Sleap failed == Removing temporary files... ACPYPE FAILED: [Errno 2] No such file or directory: 'test_AC.prmtop' So I thought that maybe the problem was my structure but even if I try this tutorial : http://code.google.com/p/acpype/wiki/TutorialAcpype4Gromacs, I obtain a similar error: === | ACPYPE: AnteChamber PYthon Parser interfacE v. 2012-09-13 14:55:47Z Rev: 389 (c) 2012 AWSdS | === == ... charge set to 0 == ... converting pdb input file to mol2 input file == * Babel OK * == Executing Antechamber... == * Antechamber OK * ++start_quote+++ /bin/sh: 1: -i: not found ++end_quote+ ERROR: Parmchk failed ERROR: Tleap failed == ... trying Sleap == Executing Sleap... ++start_quote+++ ++end_quote+ ++start_quote+++ /bin/sh: 1: -f: not found ++end_quote+ ERROR: Sleap failed == Removing temporary files... ACPYPE FAILED: [Errno 2] No such file or directory
Re: [gmx-users] Re: Problem with Amber99SB-ILDN ff
Hi there, You said ACPYPE didn't work… Can you give details? Have you try with GAFF first? If you don't mind, can you post me your molecule in private email? Thanks, Alan On 9 July 2013 22:34, Melchor S. msm...@cid.csic.es wrote: Sorry for the misunderstanding. I should had explained it better. I know that is a zwitterionic residue, I have run several simulations with the same PDB and with other forcefields. ACPYPE does not work, I tried it yesterday, but I have to check it. Antechamber I don't know, I have to try it. Also I will try to find other related parameters, but I was searching without succes. Could you suggest me something? Thanks for all your answers -- View this message in context: http://gromacs.5086.x6.nabble.com/Problem-with-Amber99SB-ILDN-ff-tp5009641p5009717.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Case sensitivity in atomtypes
I may not got the question properly but when I designed ACPYPE, I had similar issues and for that reason I created this option: -g, --disambiguatedisambiguate lower and uppercase atomtypes in GMX top file So try your usual acpype command with -g option. BTW, acpype -h can show you many more interesting options. Alan On 7 June 2013 15:55, Mark Abraham mark.j.abra...@gmail.com wrote: On Wed, Jun 5, 2013 at 11:27 AM, Baptiste Demoulin bat.demou...@gmail.comwrote: Hello GMX users, I have some troubles with overriding parameters. I have generated parameters for lipids using Lipid11 forcefield for AMBER, based on GAFF, and Acpype. This forcefield contains atomtypes cA, cB for instance. When I include the bonded parameters in [bondtypes], [angletypes] sections of my topology, or alternatively in ffbonded.itp, grompp returns warning concerning overriding of bonds and angles involving CA, CB, HA, ... (AMBER atomtypes in capital) by their equivalents in Lipid11 (cA, cB, hA, ...). WARNING 1 [file ffbonded.itp, line 222]: Overriding Bond parameters. old: 0.137 435136 0.137 435136 --- VALUE FOR AMBER FF FOR CB-CB BOND new: cB cB 11.3240e-014.9346e+05 --- VALUE FOR LIPID11 cB-cB WARNING 2 [file ffbonded.itp, line 225]: Overriding Bond parameters. old: 0.1404 392459 0.1404 392459 new: cA cB 11.5080e-012.7472e+05 WARNING 3 [file ffbonded.itp, line 227]: Overriding Bond parameters. old: 0.1381 357314 0.1381 357314 new: nA cA 11.4990e-012.4568e+05 WARNING 4 [file ffbonded.itp, line 228]: Overriding Bond parameters. old: 0.108 307106 0.108 307106 new: cA hA 11.0920e-012.8225e+05 WARNING 5 [file ffbonded.itp, line 229]: Overriding Bond parameters. old: 0.14 392459 0.14 392459 new: cA cA 11.5350e-012.5363e+05 WARNING 6 [file ffbonded.itp, line 760]: Overriding Angle parameters. old: 120 527.184 120 527.184 new: cA cA cA 11.1063e+025.2894e+02 WARNING 7 [file ffbonded.itp, line 773]: Overriding Angle parameters. old: 120 527.184 120 527.184 new: cB cA cA 11.1144e+025.3162e+02 WARNING 8 [file ffbonded.itp, line 783]: Overriding Angle parameters. old: 117.3 527.184 117.3 527.184 new: cB cB cA 11.2342e+025.3831e+02 WARNING 9 [file ffbonded.itp, line 788]: Overriding Angle parameters. old: 120 418.4 120 418.4 new: cA cA hA 11.1005e+023.8802e+02 WARNING 10 [file ffbonded.itp, line 794]: Overriding Angle parameters. old: 120 418.4 120 418.4 new: hA cA cB 11.1049e+023.9355e+02 Aren't Atomtypes supposed to be case sensitive ? Probably not, when pdb2gmx was designed. Using a case-sensitive tool like sed (or perl, or python) to re-name cA to LcA or something is probably the best solution. But don't break the fixed-column requirements of your coordinate files! Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] About AMBER Force field SB 2012 (ff12SB), using ACPYPE
With ACPYPE I can convert any Amber *.prmtop and *.crd to Gromacs, but it doesn't mean it will work straightforward (but I am working for that). For example, I am wondering how Gromacs team will port the Amber FF12SB, since now we have atom types like '2C', '3C' (ie. starting with a number), and GMX top won't accept this. Of course, a simple solution is to do '2C' - 'a2C' for example (and that works with grompp 4.6.1), but I am wondering what GMX developers would do here first, since using 3-letters wouldn't be a nice style. I am about to implement this workaround for ACPYPE, but just checking first if someone has a better idea/suggestion. Alan -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] GBSA with ligands
Hi, the issue is not with Antechamber or Acpype. There were similar questions to yours here (try searching GMX mail archives). The problem is you need to create the GBSA.itp parameters for you ligand. Which Acpype does is to create/convert Amber/GAFF parameters to usual MD in Gromacs. Alan On 12 October 2012 11:34, Leandro Bortot leandro@gmail.com wrote: Dear users, After parametrizing a ligand with antechamber and converting the topology and structure files with acpype I can't do GBSA simulations in GROMACS because of missing GB parameters. In fact, the implicit solvent parameters weren't converted from the AMBER topology (.prmtop) to the GROMACS topology (.top) by acpype. There is a FLAG RADII in the .prmtop but there is no [ implicit_genborn_params ] in the .top. Is this an issue with acpype? Any help would be greatly appreciated Best regards, Leandro -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] top/itp file to show parameters explicitly
Thanks Justin, you were right. In the end gmxdump helped to clear some doubts but I wished it would be less painfully. Cheers, Alan On 22 May 2012 12:36, Justin A. Lemkul jalem...@vt.edu wrote: On 5/22/12 12:46 PM, Alan wrote: Hi Justin, your suggestion got close. However, let me give an example. You can use the Gly-Gly-Gly example I am attaching and do this: pdb2gmx -ff amber99sb -f aGGG.pdb -o aGGG_.pdb -p aGGG.top -water none /sw/bin/grompp -c aGGG_.pdb -p aGGG.top -f SPE.mdp -o aGGG.tpr -pp aGGGp.top if you look at aGGGp.top I can't find which parameters were used for [ dihedrals ] ; aiajakal functc0c1c2 c3c4c5 2 1 5 6 9 I.e., for proper dihedral (H1- N-CA- HA1), I can't find in amber99sb.ff/forcefield.itp any combination that handles parameters for X-N-CA-X or X-CA-N-X, so how grompp is interpreting this dihedral? Make sure you're looking at types, not names. The type sequence here is H-N3-CT-HP, which I think is mapped to this dihedral: X CT N3 X 9 0.0 0.65084 3 ; JCC,7,(1986),230 Running gmxdump on the .tpr file will show it for sure; I had assumed it would be in the post-processed topology as well, but I guess not. -Justin Thanks, Alan On 21 May 2012 18:50, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: On 5/21/12 2:43 PM, Alan wrote: Hi there, Is there an option in pdb2gmx that when generating the top/itp file, it could show the parameters explicitly? e.g.: Instead of: [ dihedrals ] ; aiajakal functc0c1 c2 c3 5131112 4 11151314 4 15232122 4 21252324 4 25323133 4 (my hard hand modifications) [ dihedrals ] ; impropers ; treated as propers in GROMACS to use correct AMBER analytical function ;i j k l func phase kd pn 5 13 11 12 4 180.00 43.93200 2 ; CA- N- C- O 11 15 13 14 4 180.00 4.60240 2 ; C-CA- N- H 15 23 21 22 4 180.00 43.93200 2 ; CA- N- C- O 21 25 23 24 4 180.00 4.60240 2 ; C-CA- N- H 25 32 31 33 4 180.00 43.93200 2 ; CA- OC1- C- OC2 I mean, if the parameters that are hiding in e.g. ...gromacs/top/amber99sb.ff could be showed in the top/itp file for human readers, that would be great. You can obtain these parameters (I believe) by running grompp with the -pp option. If you think it would be a useful feature for pdb2gmx, file a feature request on redmine.gromacs.org http://redmine.gromacs.org. -Justin -- ==**__== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**__== -- gmx-users mailing list gmx-users@gromacs.org mailto: gmx-users@gromacs.org http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__**Support/Mailing_Lists/Searchhttp://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp
Re: [gmx-users] top/itp file to show parameters explicitly
Hi Justin, your suggestion got close. However, let me give an example. You can use the Gly-Gly-Gly example I am attaching and do this: pdb2gmx -ff amber99sb -f aGGG.pdb -o aGGG_.pdb -p aGGG.top -water none /sw/bin/grompp -c aGGG_.pdb -p aGGG.top -f SPE.mdp -o aGGG.tpr -pp aGGGp.top if you look at aGGGp.top I can't find which parameters were used for [ dihedrals ] ; aiajakal functc0c1c2 c3c4c5 2 1 5 6 9 I.e., for proper dihedral (H1- N-CA- HA1), I can't find in amber99sb.ff/forcefield.itp any combination that handles parameters for X-N-CA-X or X-CA-N-X, so how grompp is interpreting this dihedral? Thanks, Alan On 21 May 2012 18:50, Justin A. Lemkul jalem...@vt.edu wrote: On 5/21/12 2:43 PM, Alan wrote: Hi there, Is there an option in pdb2gmx that when generating the top/itp file, it could show the parameters explicitly? e.g.: Instead of: [ dihedrals ] ; aiajakal functc0c1c2 c3 5131112 4 11151314 4 15232122 4 21252324 4 25323133 4 (my hard hand modifications) [ dihedrals ] ; impropers ; treated as propers in GROMACS to use correct AMBER analytical function ;i j k l func phase kd pn 5 13 11 12 4 180.00 43.93200 2 ; CA- N- C- O 11 15 13 14 4 180.00 4.60240 2 ; C-CA- N- H 15 23 21 22 4 180.00 43.93200 2 ; CA- N- C- O 21 25 23 24 4 180.00 4.60240 2 ; C-CA- N- H 25 32 31 33 4 180.00 43.93200 2 ; CA- OC1- C- OC2 I mean, if the parameters that are hiding in e.g. ...gromacs/top/amber99sb.ff could be showed in the top/itp file for human readers, that would be great. You can obtain these parameters (I believe) by running grompp with the -pp option. If you think it would be a useful feature for pdb2gmx, file a feature request on redmine.gromacs.org. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 aGGG.pdb Description: Protein Databank data SPE.mdp Description: Binary data -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] missing gbsa parameters
Hi there, look at 'acpype -h', in particular: -g, --disambiguatedisambiguate lower and uppercase atomtypes in GMX top file Alan On 3 May 2012 14:34, Vedat Durmaz dur...@zib.de wrote: hi guys, i'm trying to simulate some receptor ligand system with implicit solvent using gbsa in order to get a quick folding of some tens of N-terminal peptides. this works pretty well with the target only applying the amber99sb FF. as soon as i try to simulate it together with the ligand which was parameterized with acpype (using amber-antechamber), i get the following error at the grompp step: GB parameter(s) missing or negative for atom type 'cc' GB parameter(s) missing or negative for atom type 'n' ... Fatal error: Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for 15 atomtypes or they might be negative. the atom types in the error output are exactly those listed in the [ atom types ] section of the ligand's topology file created with acpype/antechamber. however, the atom types mentioned here ARE listed in the respective gbsa.itp file which looks like this: [ implicit_genborn_params ] ; atype sar st pi gbr hct ... CC 0.1721 1.5540.18750.72 ; C does anybody know how to handle this problem? and is there someone that can tell me how (with which parameter values) to add GAFF atom types like e.g. ss, hn, hx, os to the gbsa.itp file? thanks in advance and take care vedat durmaz -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] missing gbsa parameters
Have a look at http://code.google.com/p/acpype/wiki/TutorialAcpype4Gromacs There there's a note: *NB(1):* #include Ligand.itp has to be inserted right after ffamber**.itp line and before Protein_*.itp line in *Complex.top*. Are you inserting your gbsa.itp in the *right* place of your top file? Alan On 4 May 2012 14:14, Vedat Durmaz dur...@zib.de wrote: thanks justin and alan. i also had the suspicion that the error is caused by case sensitivity. simply replacing all atom types from lower to upper case within the ligand.itp file yields the same error: missing gb parameters. using the --disambiguate option for the parameterization with acpype has exactly no effect. the generated *_GMX.itp file still contains the same lower case letters for each atom type. am i doing something wrong? when using the -atom amber option (amber99sb instead of gaff), i do get upper case types, which are not always the same as given with -a gaff. however, again, i am told by grompp, that GB parameters are missing for 15 atom types. and again, most of theese atom types ARE included in the respective gbsa.itp file (in share/gromacs/top/amber99sb.ff), but few are not. and according to those atom types that are not mentioned in grompp's error output: about half of them is listed in gbsa.itp while the other ones are not. i can't see any correlation between the atom types listed in my parameterized molecule's itp-file and the entries in gbsa.itp. does anyone have any idea? is there perhaps some other force field/database file that is checked apart from gbsa.itp?! thanks again, vedat Am 04.05.2012 11:23, schrieb Alan: Hi there, look at 'acpype -h', in particular: -g, --disambiguatedisambiguate lower and uppercase atomtypes in GMX top file Alan On 3 May 2012 14:34, Vedat Durmaz dur...@zib.de wrote: hi guys, i'm trying to simulate some receptor ligand system with implicit solvent using gbsa in order to get a quick folding of some tens of N-terminal peptides. this works pretty well with the target only applying the amber99sb FF. as soon as i try to simulate it together with the ligand which was parameterized with acpype (using amber-antechamber), i get the following error at the grompp step: GB parameter(s) missing or negative for atom type 'cc' GB parameter(s) missing or negative for atom type 'n' ... Fatal error: Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for 15 atomtypes or they might be negative. the atom types in the error output are exactly those listed in the [ atom types ] section of the ligand's topology file created with acpype/antechamber. however, the atom types mentioned here ARE listed in the respective gbsa.itp file which looks like this: [ implicit_genborn_params ] ; atype sar st pi gbr hct ... CC 0.1721 1.5540.18750.72 ; C does anybody know how to handle this problem? and is there someone that can tell me how (with which parameter values) to add GAFF atom types like e.g. ss, hn, hx, os to the gbsa.itp file? thanks in advance and take care vedat durmaz -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Acpype doubts
Hi Thales, Amber 1.5? You mean Amber12 and ambertools12? I haven't test with them yet, but it would help me if you run in the debug mode and post the output here for me: acpype -di proteinname.mol2 -c user Thanks, Alan On 26 April 2012 19:02, Thales Kronenberger kronenberg...@gmail.com wrote: I configure Amber1.5 and installed the Acpype compatible (the tests went pretty well) BUT when I tried to submit my own job by the line acpype -i proteinname.mol2 -c user i got the message: == = | ACPYPE: AnteChamber PYthon Parser interfacE v. 2011-12-19 11:11:36Z Rev: 373 (c) 2011 AWSdS | === ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp' Total time of execution: less than a second laboratorio24@laboratorio24-desktop:~/dinamicas/ATP$ it's my first time so take it easy pls ;) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Acpype Parameter Error?
Kyle, can you send and pdb file so I can reproduce your issue? Thanks, Alan On 24 February 2012 23:25, Kyle Greenway kgree...@sfu.ca wrote: Hello, This email is directed mainly to Alan, who created Acpype. I've noticed that Acpype has assigned dihedral constants as 0.65084 for many dihedrals of the form X -c3-n4-X, X -c3-c3-X, and others, in my generated GROMACS .itp files. These dihedrals have values of 1.400 in the amber 99sb .dat file, which should have instead given 1.4*4.184 = 5.858 for the result. Most other dihedrals I've checked have behaved normally and their values correspond to what would be expected - except for dihedrals with values of 0.65084 in the .itp files. Any ideas about what's going on? Thanks for your time. Kyle Greenway -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Generating topology file
I am sorry, but because antechamber will only work with these atoms: C, N, O, S, P, H, F, Cl, Br and I, so acype won't work for Hg. A hack would be to replace Hg by another allowed element. But this is only to give you a hint of what topology and parameters might look like. Then you have to work hard in literature to find parameters and likely make use of RED for getting a more quantum mechanics approach for your parameters and charges. Good luck, Alan On 23 November 2011 10:35, madhumita das madhumita.bioi...@gmail.comwrote: Hi GROMACS users, I have used acpype.py to convert parameter and topology file from amber to gromacs but some of the parameters (angle and dihedral)regarding a particular residue having mercury in it was not generating,please help. Thanks in advance. Madhumita Das -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: PDB structure quality
An update: Now for NRG-CING, please see: http://nmr.cmbi.ru.nl/NRG-CING Best, Alan On 3 April 2009 11:31, Alan alanwil...@gmail.com wrote: We've recently announced iCing, which includes whatif as well. Please, take a look at http://nmr.cmbi.ru.nl/cing/Home.html. If it happens that your complex is from NMR and deposit in PDB so you can find it here (http://nmr.cmbi.ru.nl/NRG-CING/index/index.html) already evaluated. Cheers, Alan On Fri, Apr 3, 2009 at 11:00, gmx-users-requ...@gromacs.org wrote: Chih-Ying Lin wrote: HI The program WHATIF can perform a proper validation of the structure. But, it is not free software. Can anyone tell me how to test the protein structure manually or by Gromacs? What is the criteria to determine the quality of the structure? That depends on your objective - but you have to define that. Ultimately some protein structure generated by a piece of software has to match in a relevant way the structure found in biological systems. What that means varies with what experimental information you have available. Various computational tools might assist in estimating that match. Mark -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Questionable van der waals volumes from g_sas
Hello gmx-users I have been attempting to obtain van der Waal's volumes using the g_sas utility. The command I use to do so is something like g_sas -f hexane.gro -s topol.tpr -probe 0 -tv V_vdw.xvg This seems to give reasonable results for most of my test systems, however when I run the command on an optimized structure of cyclohexane I get a larger van der Waal's volume than that of n-hexane. I think this has to do with the fact that the surface calculation method used in g_sas is missing the void in the centre of the ring. In order to test this I increased the size of the ring, calculating the volumes of icosane and cycloicosane. I found that in this case the volume of the cyclic molecule was expectedly smaller. I tried increasing the number of dots used to draw the dot-surface but saw no significant change in the volumes. Therefore my question is if anybody is familiar enough with g_sas to help me understand why the surface calculation method is not giving sensible values for these smaller ring systems. Also I am wondering if anybody can suggest any other free software that would allow me to compute van der Waal's and Solvent Excluded volumes. Thanks in advance. Jake Spooner -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] acpype generated different tip3p water paramters
Indeed, if you do the other way: 0.65084/4.184 = 0.1 ~ 0.156 Alan On 6 October 2011 08:17, Yun Shi yunsh...@gmail.com wrote: Hi Alan, So is acpype using a conversion factor of 4.184 for dihedral force constant? I found some dihedral constants as 0.156 in the amber format, which should be 0.156*4.184=0.652704 in gromacs unit. However, acpype gave a force constant of 0.65084 after conversion, which is slightly off. I wonder if this is OK, and I suspect it might be that I used rdparm to check the amber format value, which only gives 3 decimals for force constants. Thanks for the reply, Yun Hi Yun, ACPYPE is working fine. What happens here is I choose the reproduce the exact values one sees in AMBER. Now why GMX tip3p file choose a different value, I don't know. Nevertheless, it's pretty simple to put whatever value you want there if you think you need. Alan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] acpype generated different tip3p water paramters
Hi Yun, ACPYPE is working fine. What happens here is I choose the reproduce the exact values one sees in AMBER. Now why GMX tip3p file choose a different value, I don't know. Nevertheless, it's pretty simple to put whatever value you want there if you think you need. Alan On 26 September 2011 17:35, Yun Shi yunsh...@gmail.com wrote: Hi all, I just noted that the tip3p water converted from amber format to gromacs format is [ moleculetype ] ; molname nrexcl ; TIP3P model WAT 2 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 OW 1 WAT O 1 -0.834 16.0 2 HW 1 WATH1 1 0.4171.00800 3 HW 1 WATH2 1 0.4171.00800 #ifdef FLEXIBLE [ bonds ] ; i j funct length force.c. 1 2 1 0.09572 462750.4 0.09572 462750.4 1 3 1 0.09572 462750.4 0.09572 462750.4 [ angles ] ; i j k funct angle force.c. 2 1 3 1 104.520836.800 104.520836.800 #else [ settles ] ; i j funct length 1 1 0.09572 0.15139 [ exclusions ] 1 2 3 2 1 3 3 1 2 #endif while in amber99sb.ff/tip3p.itp. it is moleculetype ] ; molname nrexcl SOL 2 [ atoms ] ; id at type res nr res name at name cg nr chargemass 1 OW 1 SOL OW 1 -0.83416.0 2 HW 1 SOL HW1 1 0.417 1.00800 3 HW 1 SOL HW2 1 0.417 1.00800 #ifndef FLEXIBLE [ settles ] ; OWfunct doh dhh 1 1 0.09572 0.15139 [ exclusions ] 1 2 3 2 1 3 3 1 2 #else [ bonds ] ; i j funct length force_constant 1 2 1 0.09572 502416.0 0.09572502416.0 1 3 1 0.09572 502416.0 0.09572502416.0 [ angles ] ; i j k funct angle force_constant 2 1 3 1 104.52 628.02 104.52 628.02 #endif So it seems that the force_constants for O-H bond and H-O-H angle are different? Does this mean amber and gromacs use different parameters for tip3p water? or it's just acpype is not working right? Thanks, Yun -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: amb2gmx.pl to convert GLYCAM topology
Thanks Yun, Have a look at http://code.google.com/p/acpype/wiki/TestingAcpypeAmb2gmx so you may have tips of how to improve you check. One thing I recorded that makes diff is that amber input files have 6 decimals of precision and PDB/GRO only 3. Not knowing exactly what you did, but it sounds that 0.05% (for total pot energy?) is OK. Alan On 15 September 2011 06:18, Yun Shi yunsh...@gmail.com wrote: Hi Alan, For example, in the Glycam_06g.dat file, you can find: OH-CG-CG-OS 1 -1.10 0.0-1 So this dihedral parameter has a force constant of -1.10, and this is what I mean by GLYCAM force field assigns negative force constants to some dihedrals. I did try the GMX45 approach, and using the conversion factor 4.184, I got a difference of about 0.05%. I am not sure if this is caused not setting step size in the sander minimization. Regards, Yun Date: Tue, 13 Sep 2011 12:03:10 +0100 From: Alan alanwil...@gmail.com Subject: Re: [gmx-users] Re: amb2gmx.pl to convert GLYCAM topology To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: caeznbznq98pbhjdr1smpogdtz_pgfqsk40izlfpq7-nizyw...@mail.gmail.com Content-Type: text/plain; charset=utf-8 Hi Yun, Have you read http://ambermd.org/formats.html? In particular, this note: NOTE: *the atom numbers in the following arrays that describe bonds, angles, and dihedrals are coordinate array indexes for runtime speed. The true atom number equals the absolute value of the number divided by three, plus one. In the case of the dihedrals, if the fourth atom is negative, this implies that the dihedral is an improper. If the third atom is negative, this implies that the end group interations are to be ignored. End group interactions are ignored, for example, in dihedrals of various ring systems (to prevent double counting of 1-4 interactions) and in multiterm dihedrals. * I may be failing to understand what you mean by GLYCAM force field assigns negative force constants to some dihedrals. Anyway, since GMX 4.5 can go without RB convertions, you can do this: acpype -x disac.inpcrd -p disac.prmtop --gmx45 If you have sander, you can do just one step of EM and compare against one step EM with GMX. Do the proper conversions and Energies diff should be 0.001%. Cheers, Alan On 12 September 2011 21:21, Yun Shi yunsh...@gmail.com wrote: Hi all, I am not a CS person, but I did find something in acpype.py as . if phase in [0, 180]: properDihedralsGmx45.append([ item[0].atoms, phaseRaw, kPhi, period]) if not self.gmx45: if kPhi 0: V[period] = 2 * kPhi * cal if period == 1: C[0] += 0.5 * V[period] if phase == 0: C[1] -= 0.5 * V[period] else: C[1] += 0.5 * V[period] elif period == 2: .. kPhi here seems to be the dihedral force constant, and it seems if kPhi 0, no value will be assigned to C[0], C[1], C[2] ... I wonder if the negative dihedral force constants problem could be solved by changing 'kPhi 0' to 'kPhi != 0' for acpype? Thanks, Yun -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110913/f9bc31d1/attachment-0001.html -- Message: 5 Date: Tue, 13 Sep 2011 16:46:44 +0530 From: om prakash ombioi...@gmail.com Subject: [gmx-users] Unsubscribe me Please To: gmx-users@gromacs.org Message-ID: CAM5rxXNDPYi_aEEd+7efAmZoPex8B4Um5FwgJKg6hfm= t9y...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Unsubscribe me Please -- Om Prakash Sharma Ph.D Scholar DIT JRF Centre for Bioinformatics Pondicherry University Pondicherry-605014 -- next part -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post
Re: [gmx-users] Re: amb2gmx.pl to convert GLYCAM topology
Hi Yun, Have you read http://ambermd.org/formats.html? In particular, this note: NOTE: *the atom numbers in the following arrays that describe bonds, angles, and dihedrals are coordinate array indexes for runtime speed. The true atom number equals the absolute value of the number divided by three, plus one. In the case of the dihedrals, if the fourth atom is negative, this implies that the dihedral is an improper. If the third atom is negative, this implies that the end group interations are to be ignored. End group interactions are ignored, for example, in dihedrals of various ring systems (to prevent double counting of 1-4 interactions) and in multiterm dihedrals. * I may be failing to understand what you mean by GLYCAM force field assigns negative force constants to some dihedrals. Anyway, since GMX 4.5 can go without RB convertions, you can do this: acpype -x disac.inpcrd -p disac.prmtop --gmx45 If you have sander, you can do just one step of EM and compare against one step EM with GMX. Do the proper conversions and Energies diff should be 0.001%. Cheers, Alan On 12 September 2011 21:21, Yun Shi yunsh...@gmail.com wrote: Hi all, I am not a CS person, but I did find something in acpype.py as . if phase in [0, 180]: properDihedralsGmx45.append([item[0].atoms, phaseRaw, kPhi, period]) if not self.gmx45: if kPhi 0: V[period] = 2 * kPhi * cal if period == 1: C[0] += 0.5 * V[period] if phase == 0: C[1] -= 0.5 * V[period] else: C[1] += 0.5 * V[period] elif period == 2: .. kPhi here seems to be the dihedral force constant, and it seems if kPhi 0, no value will be assigned to C[0], C[1], C[2] ... I wonder if the negative dihedral force constants problem could be solved by changing 'kPhi 0' to 'kPhi != 0' for acpype? Thanks, Yun -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] amb2gmx.pl to convert GLYCAM topology
Or why not trying acpype?
Cheers,
Alan
On 9 September 2011 07:37, Mark Abraham mark.abra...@anu.edu.au wrote:
On 9/09/2011 4:21 PM, Yun Shi wrote:
Hi all,
I understand this problem has been discussed before, but it seems no
conclusion has been drawn.
Someone needs to do some work and report back :-)
GLYCAM force field assigns negative force constants to some dihedrals, and
when amb2gmx.pl was used to convert prmtop file to gromacs top file, these
negative values seem to be ignored. Some people proposed that we change the
code in amb2gmx.pl, that is:
...
# get all force constants for each line of a dihedral #
my $lines = $i -1 +$numijkl;
for(my $j=$i;$j=$lines;$j++){
my $period = abs($pn{$j});
if($pk{$j}0) {
$V[$period] = 2*$pk{$j}*$cal/$idivf{$j};
}
...
the $pk{$j}0 is modified to $pk{$j}!=0.
Others suggest to modify the original prmtop file, that is, to remove the
negative signs, and correspondingly, change the phase shift from 0 to 180.
Then amb2gmx.pl could be used to correctly convert the topology.
I am wondering if the first approach has been validated, since the second
one seems complicated and laborious to carry out.
Seems like a straightforward job for regular expression replacement using
sed/perl/python/whatever. It might even be a one-liner.
Mark
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[gmx-users] question regarding g_energy -aver output in gromacs 4.5.4
Dear gmx_users, I have a question regarding the 4.5.4 version of gromacs, and the g_energy program. In the past I had used g_energy with the -aver option, which would give me partial sums along with my instantaneous energy values at each output step. This allowed me to take the difference between two successive partial sums divided by the my nstenergy value to get the average energy over that output period. Now when I use the -aver option my output contains my instantaneous value, and what is said to be the exact average. I have the feeling that this exact average is what I used to calculate by hand, i.e the average of the energy over each output period. I tried to test this by calculating the average by hand using gmxdump and my ener.edr file and my numbers match up to the fourth decimal place, but aren't exactly the same. Is this difference simply because gmxdump is truncating the energy values and giving them to me at lower precision? Am I correct on my assumption of what this -aver option is giving me? Any guidance would be appreciated as I'm not so good at understanding the source code. Thank you in advance Jake Spooner -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Acpype error
Hi Liao, Your python installation seems to be missing the datetime module, which is very bizarre. Please verify your Python installation, you may have issues with your PYTHONPATH. Regards, Alan 2011/4/12 fancy2012 fancy2...@yeah.net Hi GMX users, When I ran acpype.py on my computer, I got one error like this: File ./acpype.py, line 67, in module from datetime import datetime ImportError: No module named datetime I use Python-2.6.6, I do not know how this error happen, could someone help me figure it out? Thanks very much in advance! -- *Best wishes,* *Qinghua Liao* *Ph.D student of Tianjin University, China* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] converting ILDN parameters to RB
Hi there, Since ILDN dihedrals has some parameters with up to periodicity 6, I was wondering if it's possible to convert it in RB with 6 coefficients. If so, what would be the formula? For example, for converting the usual Amber99SB to RB I have: if phase in [0, 180]: if kPhi 0: V[period] = 2 * kPhi * cal if period == 1: C[0] += 0.5 * V[period] if phase == 0: C[1] -= 0.5 * V[period] else: C[1] += 0.5 * V[period] elif period == 2: if phase == 180: C[0] += V[period] C[2] -= V[period] else: C[2] += V[period] elif period == 3: C[0] += 0.5 * V[period] if phase == 0: C[1] += 1.5 * V[period] C[3] -= 2 * V[period] else: C[1] -= 1.5 * V[period] C[3] += 2 * V[period] elif period == 4: if phase == 180: C[2] += 4 * V[period] C[4] -= 4 * V[period] else: C[0] += V[period] C[2] -= 4 * V[period] C[4] += 4 * V[period] So, as you can see, I can handle up to 4 periods (C[5] is always 0, but not with ILDN and I need to add C[6] rules as well). Any ideas? Many thanks in advance, Alan -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] converting ILDN parameters to RB
I know it's supported. I was just investigating the possibility since I build acpype to create topologies for gromacs, but also it converts from amber to gromacs (like amb2gmx.pl), and so I was wondering about RB with 6 coefficients since multiple proper dihedrals is only supported for gmx 4.5 and above. But I don't want to fuss about it. If to forget about GMX 4.0.x and below is the way, so it will be. Thanks, Alan On 31 March 2011 16:08, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2011-03-31 15.27, Alan Wilter Sousa da Silva wrote: Hi there, Since ILDN dihedrals has some parameters with up to periodicity 6, I was wondering if it's possible to convert it in RB with 6 coefficients. If so, what would be the formula? For example, for converting the usual Amber99SB to RB I have: ILDN is already supported in the latest gromacs releases, by simply using multiple proper dihedrals. Why would you want to change it? if phase in [0, 180]: if kPhi 0: V[period] = 2 * kPhi * cal if period == 1: C[0] += 0.5 * V[period] if phase == 0: C[1] -= 0.5 * V[period] else: C[1] += 0.5 * V[period] elif period == 2: if phase == 180: C[0] += V[period] C[2] -= V[period] else: C[2] += V[period] elif period == 3: C[0] += 0.5 * V[period] if phase == 0: C[1] += 1.5 * V[period] C[3] -= 2 * V[period] else: C[1] -= 1.5 * V[period] C[3] += 2 * V[period] elif period == 4: if phase == 180: C[2] += 4 * V[period] C[4] -= 4 * V[period] else: C[0] += V[period] C[2] -= 4 * V[period] C[4] += 4 * V[period] So, as you can see, I can handle up to 4 periods (C[5] is always 0, but not with ILDN and I need to add C[6] rules as well). Any ideas? Many thanks in advance, Alan -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: [ atomtypes ] are not case sensitive?
Dear GMX list, It's more the 2 years ago and now with my gmx.top file containing: [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb CA CA 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 caca 0. 0. A 3.39967e-01 3.59824e-01 And using GMX 4.5 and I don't see this complain anymore: WARNING 1 [file system_GMX.top, line 43]: Overriding atomtype CA Should I assume that gromacs finally made its atomtypes case sensitive? Only version 4.5 and above? Many thanks, Alan On 21 August 2008 09:07, Alan alanwil...@gmail.com wrote: Well, I didn't developed Amber FF neither GAFF and although only Amber FF is ported to GMX, one of the greatest appealing of Amber is its antechamber and GAFF for generating topology for non usual compounds. Looking at the way GAFF was developed (remember G is for generalised) is seemed a natural step to me to use the same name for atom types but using a different cases. So have said that, I did a look at my converted topology file by amb2gmx/acpypi and found that, although for vdw parameters they seem the same, this doesn't hold for bonds for example. I have this in my GMX top file: [ bonds ] ... 96 97 11.0800e-013.0711e+05 ;CZ2 - HZ2 (AT CA - HA) Protein ... 3154 3194 11.0870e-012.8811e+05 ;C76 - H76 (AT ca - ha) Ligand Anyway, after all this discussion, I realized (correct if I am wrong please) that as long as the vdw parameters are the same, anything else is NOT affected because even for the example of bonds above atom types change nothing since parameters are explicit. Then, I decided to compare gaff.dat and parm99.dat (topology parameters files for Amber package) for vdw. I did found 2 atom types with same name (diff case though) and diff parameters: parm99.dat HP 1.1000 0.0157 Veenstra et al JCC,8,(1992),963 Na 1.8680 0.00277Na+ Aqvist JPC 1990,94,8021. (adapted) gaff.dat hp 0.6000 0.0157 same to hs (be careful !) na 1.8240 0.1700 OPLS Observe by the comments (4th column) that although they have the same name (but diff by case) they are completely unrelated, hence the diff values for r0 and epsilon. So, in the end, at least for example gaff.dat x parm99.dat (note that Amber has several others parm*.dat and glycam*.dat), I do have a conflicting case issue that would affect my topology in GMX format if using amb2gmx/acpypi tool for conversion. Pondering a bit more, I came to the conclusion that at least for acpypi (which I am developing), I can make it aware of this conflicting atom type naming issue and rename it when converting from Amber to GMX. About changing something in GMX? Frankly I don't know, but I hope that this thread can be of some use for someone else who stumbles in this problem. Cheers and many thanks for attention dear Berk. Alan From: Berk Hess g...@hotmail.com Subject: RE: [gmx-users] RE: [ atomtypes ] are not case sensitive? Hi, I don't know if any thinking went into the (non) case specifity of atom types. Nearly all string comparisons in Gromacs are not case specific. For things like atom names this makes sense. We could change the atom type comparisons to case specific. I think that all force field files supplied with Gromacs have consistent cases. But some users might have made force fields where this would cause problems. I think it is bad practice to distinguish atom types just by case, this makes things quite error prone. But allowing this probably does not mean that many people would do this. Another option would be to add an option to grompp. Berk. Date: Tue, 19 Aug 2008 12:03:57 +0100 From: alanwil...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] RE: [ atomtypes ] are not case sensitive? Dear Berk, Thanks for your attention. I don't know how familiar are you to amb2gmx and ffamber port to GMX. I am just learning since I am trying to test an application that is related to amb2gmx and ffamber (acpypi). So, for Amber MD (MD to contrast with FF), Generalised Amber Force Field (GAFF) uses all the atom types (AT) usually defined for Amber FF and several more AT but in lower case. I cannot assure 100% but I believe that for all common AT (being upper or lower), they share the same parameters including when found in bonds, angles etc. parameters. If so, then, it's not a problem if GMX is not sensitive about AT lower or upper case, because in the end they are the same. But, as I said before, I am not 100% sure about it. However, for Amber MD, case matters! Anyway, I am just worried about integrating Amber FF in GMX. If using ffamber port this problem doesn't appear because for Amber FF (ffamber*.itp files in GMX/top folder), AT are defined as, e.g., 'amber99_27', and so if I add a ligand.itp build
Re: [gmx-users] amber convert gromacs input files
Have a good look in acpype, specially its wiki. There you'll see that acpype is totally new code and among other things it covers amb2gmx.pl and solves several of its drawbacks. It's not perfect though but for a system created in tleap, the project is likely to be completed converted to gmx. Alan On 23 December 2010 22:29, Oliver Grant olymacfoo...@gmail.com wrote: Hi, Not sure exactly what you plan to simulate but here are a couple of potential pitfalls: Does acpype call amb2gmx.pl or is it new code that converts? If it is a amb2gmx.pl call I'd check the torsions on the NAc group if you have one. They didn't get translated when I used it. When using amber ports be careful about using default index groups like protein or C alpha as they won't contain atoms from residues like LYP that are different in the ports. Also you'll want to set fudge to 1.0 in the amber99sb.itp or where it is set (can't check this atm) if simulating the sugar alone. Its due to differences in the way amber and glycam are parametrized. (If you are interested it is differences in 1-4 scaling). There may be other issues I'm not aware of yet. :) All the best, Oliver On 23 December 2010 18:13, Alan Wilter Sousa da Silva awil...@ebi.ac.ukwrote: Have a look at acpype.googlecode.com Alan 2010/12/23 gromacs564 gromacs...@126.com Hi , I have obtained some files(.top,.crd,.pdb) about disaccharide via glycam web(they are glycam06 force field,included in AMBER) , but cannot converted this amber files to gromacs files format. Can anyone help me to convert this (amber) files to gromacs input files(top or itp,gro).? Many thanks! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Alan Wilter SOUSA da SILVA, D.Sc. Bioinformatician, UniProt - PANDA, EBI-EMBL CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Alan Wilter SOUSA da SILVA, D.Sc. Bioinformatician, UniProt - PANDA, EBI-EMBL CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] amber convert gromacs input files
Have a look at acpype.googlecode.com Alan 2010/12/23 gromacs564 gromacs...@126.com Hi , I have obtained some files(.top,.crd,.pdb) about disaccharide via glycam web(they are glycam06 force field,included in AMBER) , but cannot converted this amber files to gromacs files format. Can anyone help me to convert this (amber) files to gromacs input files(top or itp,gro).? Many thanks! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Alan Wilter SOUSA da SILVA, D.Sc. Bioinformatician, UniProt - PANDA, EBI-EMBL CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] MD on docked complex using AMBER FF
Also, have a read at acpype.googlecode.com. Alan On 21 September 2010 06:36, manoj singh mks.am...@gmail.com wrote: First, you have to develop parameter for your molecule withing Amber. Then you have to create .prmtop and .inpcrd files for your molecule, and than you can convert the Amber topology to Gromacs topology. You will need AmberTools and a script called amb2gmx.pl. Following links would be helpful for you http://ambermd.org/#AmberTools http://ambermd.org/antechamber/efz.html ffamber.cnsm.csulb.edu/*amb2gmx*.*pl* On Tue, Sep 21, 2010 at 12:51 AM, vivek sharma viveksharma.i...@gmail.com wrote: Hi There, I am trying to run molecular dynamics on a drug-enzyme complex using amber force field. I have done it earlier using gromos FF using drug-enzyme tutorial, I dont know if the parameter set (.mdp file) will be same or different while using AMBER FF. Any insight/comments into the matter may be of help if somebody has tried using AMBER FF for docked complex in GROMACS. Thanks in advance. regards, Vivek -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] MD on docked complex using AMBER FF
I do recommend amber ff99sb, but have a read in some papers that is referred in acpype website. Also, getting the mdp file tuned will require testing. The mdp you see in acpype website are examples that work but surely need tweaking for production and for that I recommend you to read gmx manual carefully. Then you can come with more specific questions. Alan On 21 September 2010 08:03, vivek sharma viveksharma.i...@gmail.com wrote: Hi, Thanks Manoj and Alan for your quick response. I am already using the ambertools to generate the topology and these topologies are successfully accepted in gromacs. I will have a look at alternate methodologies and workflow that you guys have suggested. My question is can I have any idea that which version of AMBER FF should be used in this case of drug-enzyme complex? Also, can I have any idea about the selection of MD parameters, (which goes in mdp file) that should be used in this case? With thanks, Vivek On 21 September 2010 12:24, Alan alanwil...@gmail.com wrote: Also, have a read at acpype.googlecode.com. Alan On 21 September 2010 06:36, manoj singh mks.am...@gmail.com wrote: First, you have to develop parameter for your molecule withing Amber. Then you have to create .prmtop and .inpcrd files for your molecule, and than you can convert the Amber topology to Gromacs topology. You will need AmberTools and a script called amb2gmx.pl. Following links would be helpful for you http://ambermd.org/#AmberTools http://ambermd.org/antechamber/efz.html ffamber.cnsm.csulb.edu/amb2gmx.pl On Tue, Sep 21, 2010 at 12:51 AM, vivek sharma viveksharma.i...@gmail.com wrote: Hi There, I am trying to run molecular dynamics on a drug-enzyme complex using amber force field. I have done it earlier using gromos FF using drug-enzyme tutorial, I dont know if the parameter set (.mdp file) will be same or different while using AMBER FF. Any insight/comments into the matter may be of help if somebody has tried using AMBER FF for docked complex in GROMACS. Thanks in advance. regards, Vivek -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] an example to test mdrun-gpu x mdrun
Hi there, I am testing on a MBP 17 SL 10.6.4 64 bits and nvidia GeForce 9600M GT So I got mdrun-gpu compiled and apparently running, but when I try to run 'mdrun' to compare I have a segment fault. Any other comments to the md.mdp and em.mdp are very welcome too. # To test mdrun-gpu cat EOF | em.mdp define = -DFLEXIBLE integrator = cg ; steep nsteps = 200 constraints = none emtol= 1000.0 nstcgsteep = 10 ; do a steep every 10 steps of cg emstep = 0.01 ; used with steep nstcomm = 1 coulombtype = PME ns_type = grid rlist= 1.0 rcoulomb = 1.0 rvdw = 1.4 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 0 ; write coords every # step optimize_fft = yes EOF cat EOF | md.mdp integrator = md-vv nsteps = 1000 dt = 0.002 constraints = all-bonds constraint-algorithm = shake nstcomm = 1 nstcalcenergy= 1 ns_type = grid rlist= 1.3 rcoulomb = 1.3 rvdw = 1.3 vdwtype = cut-off coulombtype = PME Tcoupl = Andersen nsttcouple = 1 tau_t= 0.1 tc-grps = system ref_t= 300 Pcoupl = mttk Pcoupltype = isotropic nstpcouple = 1 tau_p= 0.5 compressibility = 4.5e-5 ref_p= 1.0 gen_vel = yes nstxout = 2 ; write coords every # step lincs-iter = 2 DispCorr = EnerPres optimize_fft = yes EOF wget -c http://www.pdbe.org/download/1brv; -O 1brv.pdb pdb2gmx -ff amber99sb -f 1brv.pdb -o Prot.pdb -p Prot.top -water spce -ignh editconf -bt triclinic -f Prot.pdb -o Prot.pdb -d 1.0 genbox -cp Prot.pdb -o Prot.pdb -p Prot.top -cs grompp -f em.mdp -c Prot.pdb -p Prot.top -o Prot.tpr echo 13 | genion -s Prot.tpr -o Prot.pdb -neutral -conc 0.15 -p Prot.top -norandom grompp -f em.mdp -c Prot.pdb -p Prot.top -o em.tpr mdrun -v -deffnm em grompp -f md.mdp -c em.gro -p Prot.top -o md.tpr mdrun-gpu -v -deffnm md -device OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes [snip] Reading file md.tpr, VERSION 4.5.1-dev-20100913-9342b (single precision) Loaded with Money Back Off! I just backed up md.trr to ./#md.trr.7# Back Off! I just backed up md.edr to ./#md.edr.7# WARNING: OpenMM supports only Andersen thermostat with the md/md-vv/md-vv-avek integrators. WARNING: OpenMM supports only Monte Carlo barostat for pressure coupling. WARNING: Non-supported GPU selected (#0, GeForce 9600M GT), forced continuing.Note, that the simulation can be slow or it migth even crash. Pre-simulation ~15s memtest in progress...done, no errors detected starting mdrun 'PROTEIN G in water' 1000 steps, 2.0 ps. step 900, remaining runtime: 4 s Writing final coordinates. step 1000, remaining runtime: 0 s Post-simulation ~15s memtest in progress...done, no errors detected OpenMM run - timing based on wallclock. NODE (s) Real (s) (%) Time: 44.556 44.556100.0 (Mnbf/s) (MFlops) (ns/day) (hour/ns) Performance: 0.000 0.027 3.882 6.182 But if I try: mdrun -v -deffnm md -nt 1 [snip] starting mdrun 'PROTEIN G in water' 1000 steps, 2.0 ps. [1]75786 segmentation fault mdrun -v -deffnm md -nt 1 Note: using -nt 1 because SHAKE is not supported with domain decomposition. If using Tcoupl and Pcoupl = no and then I can compare mdrun x mdrun-gpu, being my gpu ~2 times slower than only one core. Well, I definitely don't intended to use mdrun-gpu but I am surprised that it performed that bad (OK, I am using a low-end GPU, but sander_openmm seems to work fine and very fast on my mbp). BTW, in gmx 4.5 manual, there's reference to Andersen thermostat only at section 6.9 GROMACS on GPUs. Is it supposed to be used only with mdrun-gpu? Any ideas? Thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] please help, cannot compile gmx 4.5 openmm
Dear Rossen, Thanks for your reply. For your info I use Mac 10.6 with Fink in 64 bits. I have access to svn Openmm dev source code so I am compiling it in 64 bits. It could be a source of issues, but all others programmes I have running that depends on openmm (e.g. sander_openmm) were working fine except GMX. Bizzarely but gmx 4.5 beta were compiling ok. I will try release-4-5-patches updated later. Thanks, Alan On 13 September 2010 12:58, Rossen Apostolov ros...@kth.se wrote: Just to add: the pre-built OpenMM-2.0 for Mac are compiled for 32bit. If you get an error as: Linking CXX shared library libopenmm_api_wrapper.dylib ld: warning: in /usr/local/openmm/lib/libOpenMM.dylib, file was built for i386 which is not the architecture being linked (x86_64) Undefined symbols: OpenMM::State::getVelocities() const, referenced from: snip . then you can force compilation for 32bit by: $ export CFLAGS='-arch i386' $ export CXXFLAGS='-arch i386' or recompile the openmm from source. Rossen On 9/13/10 1:01 PM, Rossen Apostolov wrote: Hi Alan, There was a missing dependency for building gmx_gpu_utils, but for some reason compilation didn't break on linux:) This is now fixed in release-4-5-patches. Pay attention though that the prebuilt OpenMM-2.0 libraries from the SimTK website are for MacOSX 10.6 Rossen On 9/11/10 12:56 AM, Alan wrote: I am doing, after compiling and installing the normal grmx 4.5: rm -fr CMakeCache.txt make clean export OPENMM_ROOT_DIR=/usr/local/openmm cmake -DGMX_OPENMM=ON .. make mdrun [ 1%] Building NVCC (Device) object src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_memtestG80_core.cu.o [ 1%] Building NVCC (Device) object src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_gmx_gpu_utils.cu.o Scanning dependencies of target gmx_gpu_utils Linking CXX shared library libgmx_gpu_utils.dylib Undefined symbols: _gmx_strncasecmp, referenced from: is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o _debug, referenced from: is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o do_timed_memtest(int, int)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o do_full_memtest(int) in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o do_quick_memtest(int) in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o _trim, referenced from: is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o ld: symbol(s) not found collect2: ld returned 1 exit status make[3]: *** [src/kernel/gmx_gpu_utils/libgmx_gpu_utils.dylib] Error 1 make[2]: *** [src/kernel/gmx_gpu_utils/CMakeFiles/gmx_gpu_utils.dir/all] Error 2 make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2 make: *** [mdrun] Error 2 -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 http://www.bio.cam.ac.uk/%7Eawd28 -- -Rossen -- -Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search
[gmx-users] please help, cannot compile gmx 4.5 openmm
I am doing, after compiling and installing the normal grmx 4.5: rm -fr CMakeCache.txt make clean export OPENMM_ROOT_DIR=/usr/local/openmm cmake -DGMX_OPENMM=ON .. make mdrun [ 1%] Building NVCC (Device) object src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_memtestG80_core.cu.o [ 1%] Building NVCC (Device) object src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_gmx_gpu_utils.cu.o Scanning dependencies of target gmx_gpu_utils Linking CXX shared library libgmx_gpu_utils.dylib Undefined symbols: _gmx_strncasecmp, referenced from: is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o _debug, referenced from: is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o do_timed_memtest(int, int)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o do_full_memtest(int) in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o do_quick_memtest(int) in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o _trim, referenced from: is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o ld: symbol(s) not found collect2: ld returned 1 exit status make[3]: *** [src/kernel/gmx_gpu_utils/libgmx_gpu_utils.dylib] Error 1 make[2]: *** [src/kernel/gmx_gpu_utils/CMakeFiles/gmx_gpu_utils.dir/all] Error 2 make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2 make: *** [mdrun] Error 2 -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] pdb2gmx gmx 4.5: issues with atom name in last column
Hi there, when using for example: pdb2gmx -f aQQQ.pdb -o agQQQ.pdb -p agQQQ.top -ff amber99sb -water none I got in the agQQQ.pdb, things like: ATOM 15 NE2 NGL 1 4.309 7.159 2.648 1.00 0.00 N ATOM 16 1HE2 NGL 1 4.030 7.698 3.448 1.00 0.00 HE ATOM 17 2HE2 NGL 1 5.066 7.449 2.048 1.00 0.00 HE ATOM 18 C NGL 1 5.487 2.636 0.037 1.00 0.00 C Notice the last column, in special the HE. This is wrong! For most programmes it's not a issue since they seem to ignore the last column but this column exist and has a propose. And there programmes that observe this column, like openbabel. If converting this pdb to mol2 I got wrong structure since babel thinks I am dealing with Helium atoms. In gmx 4.0.x the last column was never printed so never had this problem before. Thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] git gromacs
Hi there, Now that gromacs 4.5.1 is released I was wondering which branch should I checkout if I want to test the bleeding edge gromacs development. Thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] git gromacs
Thanks Carsten. I am trying release-4-5-patches and now I can see it's compiling and installing. However, 'make install' puts the bins only in /usr/local/gromacs/bin and I don't have (or don't find) how to 'make links' or similar to have the gmx bins in /usr/local/bin. I am using cmake. Thanks, Alan On 7 September 2010 11:57, Carsten Kutzner ckut...@gwdg.de wrote: Hi Alan, 'bleeding edge' gromacs development is as always in the 'master' branch. The latest bugfixes for the 4.5.x versions you are going to find in the 'release-4-5-patches' branch. Carsten On Sep 7, 2010, at 12:09 PM, Alan wrote: Hi there, Now that gromacs 4.5.1 is released I was wondering which branch should I checkout if I want to test the bleeding edge gromacs development. Thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] git gromacs
If using links or simply copying in /usr/local/bin I don't mind, but it would easier, at least for me, once installing gromacs from source to be able to have the gmx bins in /usr/local/bin and, of course, be able to uninstall all gromacs as well (and undoing links or removing copies from /usr/local/bin). Of course, I can just put another path in $PATH, although I do not prefer this solution: one reason, I have all my scripts and testing sets looking at /usr/local/bin. Yet, I can fix this... but oh boy. Anyway, I took this former approach because somehow one of gmx 4.5 betas was installing gmx bin in /usr/local/bin. I praise consistency. Thanks, Alan On 7 September 2010 13:05, Rossen Apostolov rossen.aposto...@cbr.su.sewrote: On 9/7/10 1:19 PM, Alan wrote: I am trying release-4-5-patches and now I can see it's compiling and installing. However, 'make install' puts the bins only in /usr/local/gromacs/bin and I don't have (or don't find) how to 'make links' or similar to have the gmx bins in /usr/local/bin. I am using cmake. CMake doesn't have a 'make links' target yet. Are there a lot of people who actually use it? Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] gmx 4.5.1 and opemm not compiling on Mac SL
Hi there, I am trying: ~/Downloads/gromacs-4.5.1/build% cmake -DGMX_OPENMM=ON .. ~/Downloads/gromacs-4.5.1/build% make mdrun [ 1%] Building NVCC (Device) object src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_memtestG80_core.cu.o [ 1%] Building NVCC (Device) object src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_gmx_gpu_utils.cu.o Scanning dependencies of target gmx_gpu_utils Linking CXX shared library libgmx_gpu_utils.dylib Undefined symbols: _gmx_strncasecmp, referenced from: is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o _debug, referenced from: is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o do_timed_memtest(int, int)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o do_full_memtest(int) in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o do_quick_memtest(int) in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o _trim, referenced from: is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o is_supported_cuda_gpu(int, char*)in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o ld: symbol(s) not found collect2: ld returned 1 exit status make[3]: *** [src/kernel/gmx_gpu_utils/libgmx_gpu_utils.dylib] Error 1 make[2]: *** [src/kernel/gmx_gpu_utils/CMakeFiles/gmx_gpu_utils.dir/all] Error 2 make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2 make: *** [mdrun] Error 2 Same thing with gmx from git. Any idea? Thanks. Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now
Just one more question. How are you handling CYS? In amber it could be CYP, CYN etc. Thanks a lot, Alan On 25 August 2010 13:59, Berk Hess g...@hotmail.com wrote: Hi, I now turned on the automatic HIE, and analogous, terminal renaming on by default. Berk -- From: g...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now Date: Wed, 25 Aug 2010 14:34:30 +0200 Hi, I fixed all the terminal residue issues. The automatic HIE terminal translation is still swtiched by the env.var. I'm still thinking if there could be issues when we turn that always on. Berk -- From: alanwil...@gmail.com Date: Tue, 24 Aug 2010 22:55:57 +0100 Subject: Re: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now To: gmx-users@gromacs.org Dear Berk, I understand your point and this can be very confusing. I am aware that I could use HIS and then pdb2gmx ... -his (option 1), but this is not working either with rev. d6298. Error: [snip] Which HISTIDINE type do you want for residue 3 0. H on ND1 only (HID) 1. H on NE2 only (HIE) 2. H on ND1 and NE2 (HIP) 3. Coupled to Heme (HIS1) Type a number:1 Identified residue HIS1 as a starting terminus. Identified residue HIS3 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS1HIS2 NE214 NE231 HIS2 NE231 0.854 HIS3 NE248 0.751 0.847 --- Program pdb2gmx, VERSION 4.5-beta3-dev-20100824-d6298 Source code file: /Users/alan/workspace/gromacs/src/kernel/resall.c, line: 552 Fatal error: Residue 'HISE' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors The pdb I am using is hhh.pdb ATOM 1 N HIS 1 3.389 1.609 -0.001 1.00 0.00 N ATOM 2 H1 HIS 1 4.107 0.893 -0.048 1.00 0.00 H ATOM 3 H2 HIS 1 2.795 1.549 -0.816 1.00 0.00 H ATOM 4 H3 HIS 1 2.844 1.452 0.836 1.00 0.00 H ATOM 5 CA HIS 1 4.058 2.928 0.075 1.00 0.00 C ATOM 6 HA HIS 1 3.894 3.469 -0.857 1.00 0.00 H ATOM 7 CB HIS 1 3.469 3.750 1.230 1.00 0.00 C ATOM 8 HB2 HIS 1 2.384 3.783 1.126 1.00 0.00 H ATOM 9 HB3 HIS 1 3.695 3.231 2.164 1.00 0.00 H ATOM 10 CG HIS 1 3.956 5.172 1.373 1.00 0.00 C ATOM 11 ND1 HIS 1 4.013 5.834 2.591 1.00 0.00 N ATOM 12 CE1 HIS 1 4.604 7.011 2.356 1.00 0.00 C ATOM 13 HE1 HIS 1 4.832 7.752 3.115 1.00 0.00 H ATOM 14 NE2 HIS 1 4.919 7.122 1.056 1.00 0.00 N ATOM 15 HE2 HIS 1 5.505 7.845 0.657 1.00 0.00 H ATOM 16 CD2 HIS 1 4.479 5.987 0.403 1.00 0.00 C ATOM 17 HD2 HIS 1 4.620 5.781 -0.645 1.00 0.00 H ATOM 18 C HIS 1 5.564 2.693 0.196 1.00 0.00 C ATOM 19 O HIS 1 5.947 1.551 0.422 1.00 0.00 O ATOM 20 N HIS 2 6.376 3.718 -0.053 1.00 0.00 N ATOM 21 H HIS 2 5.980 4.646 -0.135 1.00 0.00 H ATOM 22 CA HIS 2 7.843 3.744 -0.109 1.00 0.00 C ATOM 23 HA HIS 2 8.260 3.319 0.806 1.00 0.00 H ATOM 24 CB HIS 2 8.319 2.925 -1.327 1.00 0.00 C ATOM 25 HB2 HIS 2 7.855 1.940 -1.312 1.00 0.00 H ATOM 26 HB3 HIS 2 7.985 3.435 -2.233 1.00 0.00 H ATOM 27 CG HIS 2 9.807 2.703 -1.450 1.00 0.00 C ATOM 28 ND1 HIS 2 10.461 2.463 -2.655 1.00 0.00 N ATOM 29 CE1 HIS 2 11.770 2.542 -2.382 1.00 0.00 C ATOM 30 HE1 HIS 2 12.557 2.484 -3.124 1.00 0.00 H ATOM 31 NE2 HIS 2 11.969 2.794 -1.078 1.00 0.00 N ATOM 32 HE2 HIS 2 12.817 3.173 -0.672 1.00 0.00 H ATOM 33 CD2 HIS 2 10.740 2.839 -0.459 1.00 0.00 C ATOM 34 HD2 HIS 2 10.579 3.098 0.574 1.00 0.00 H ATOM 35 C HIS 2 8.279 5.228 -0.214 1.00 0.00 C ATOM 36 O HIS 2 7.440 6.079 -0.525 1.00 0.00 O ATOM 37 N HIS 3 9.547 5.520 0.075 1.00 0.00 N ATOM 38 H HIS 3 10.192 4.759 0.245 1.00 0.00 H ATOM 39 CA HIS 3 10.254 6.807 0.049 1.00 0.00 C ATOM 40 HA HIS 3 10.021 7.358 -0.860 1.00 0.00 H ATOM 41 CB HIS 3 9.841 7.621 1.297 1.00 0.00 C ATOM 42 HB2 HIS
Re: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now
Not really, I mentioned that based on Sorin's ffamber page: a) Non-terminal amino and nucleic acid residues follow standard AMBER naming conventions. To avoid confusion between GROMACS and AMBER conventions, we have omitted the redundant HIS residue, leaving HID, HIE, HIP, and terminal versions of these topologies. Additionally, due to the automated changing of certain residue names by pdb2gmx, the LYS and CYS residues have been renamed LYP (Lysine plus) and CYN (Cysteine neutral, compared to AMBER residue CYM = Cysteine minus). (b) C- and N-terminal amino acids include a C or N prefix respectively, so C-terminal ALA is CALA and N-ternimal PHE is NPHE. As with non-terminal versions, the LYS and CYS terminal residues are listed as NLYP,CLYP and NCYN,CCYN. And I did mistake, it's not CYP, but CYN. So I don't know if you are fully following Sorin's recommendations. On 25 August 2010 14:36, Berk Hess g...@hotmail.com wrote: You can find the residue name to rtp translation table in: share/top/amber99.ff/aminoacids.r2b I don't have a list with Amber names and funtions for the amino acids. Currently for Amber in Gromacs we have CYS (standard, neutral, protonated) and CYX (disulfide bond). Does Amber use CYP instead of CYS? Berk -- From: alanwil...@gmail.com Date: Wed, 25 Aug 2010 14:17:58 +0100 Subject: Re: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now To: gmx-users@gromacs.org Just one more question. How are you handling CYS? In amber it could be CYP, CYN etc. Thanks a lot, Alan On 25 August 2010 13:59, Berk Hess g...@hotmail.com wrote: Hi, I now turned on the automatic HIE, and analogous, terminal renaming on by default. Berk -- From: g...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now Date: Wed, 25 Aug 2010 14:34:30 +0200 Hi, I fixed all the terminal residue issues. The automatic HIE terminal translation is still swtiched by the env.var. I'm still thinking if there could be issues when we turn that always on. Berk -- From: alanwil...@gmail.com Date: Tue, 24 Aug 2010 22:55:57 +0100 Subject: Re: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now To: gmx-users@gromacs.org Dear Berk, I understand your point and this can be very confusing. I am aware that I could use HIS and then pdb2gmx ... -his (option 1), but this is not working either with rev. d6298. Error: [snip] Which HISTIDINE type do you want for residue 3 0. H on ND1 only (HID) 1. H on NE2 only (HIE) 2. H on ND1 and NE2 (HIP) 3. Coupled to Heme (HIS1) Type a number:1 Identified residue HIS1 as a starting terminus. Identified residue HIS3 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS1HIS2 NE214 NE231 HIS2 NE231 0.854 HIS3 NE248 0.751 0.847 --- Program pdb2gmx, VERSION 4.5-beta3-dev-20100824-d6298 Source code file: /Users/alan/workspace/gromacs/src/kernel/resall.c, line: 552 Fatal error: Residue 'HISE' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors The pdb I am using is hhh.pdb ATOM 1 N HIS 1 3.389 1.609 -0.001 1.00 0.00 N ATOM 2 H1 HIS 1 4.107 0.893 -0.048 1.00 0.00 H ATOM 3 H2 HIS 1 2.795 1.549 -0.816 1.00 0.00 H ATOM 4 H3 HIS 1 2.844 1.452 0.836 1.00 0.00 H ATOM 5 CA HIS 1 4.058 2.928 0.075 1.00 0.00 C ATOM 6 HA HIS 1 3.894 3.469 -0.857 1.00 0.00 H ATOM 7 CB HIS 1 3.469 3.750 1.230 1.00 0.00 C ATOM 8 HB2 HIS 1 2.384 3.783 1.126 1.00 0.00 H ATOM 9 HB3 HIS 1 3.695 3.231 2.164 1.00 0.00 H ATOM 10 CG HIS 1 3.956 5.172 1.373 1.00 0.00 C ATOM 11 ND1 HIS 1 4.013 5.834 2.591 1.00 0.00 N ATOM 12 CE1 HIS 1 4.604 7.011 2.356 1.00 0.00 C ATOM 13 HE1 HIS 1 4.832 7.752 3.115 1.00 0.00 H ATOM 14 NE2 HIS 1 4.919 7.122 1.056 1.00 0.00 N ATOM 15 HE2 HIS 1 5.505 7.845 0.657 1.00 0.00 H ATOM 16 CD2 HIS 1 4.479 5.987 0.403 1.00 0.00 C ATOM 17 HD2 HIS 1 4.620 5.781 -0.645 1.00 0.00 H ATOM 18 C HIS 1 5.564 2.693 0.196 1.00 0.00 C ATOM 19 O HIS 1 5.947 1.551 0.422 1.00 0.00 O ATOM 20 N HIS 2 6.376 3.718 -0.053 1.00 0.00 N ATOM 21 H HIS 2 5.980 4.646 -0.135 1.00 0.00 H ATOM 22 CA
Re: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now
Ah, great. Thanks Berk. FYI, because I am developing a tool (ACPYPE) and I wrote the test using gromacs and ff oplsaa and amber so that's why it's relatively easy and quick to test and check the issues I was having. But it also happens that I am adapting my test code for gmx 4.5 and so I bump in some problems, 99% my fault of course. Thanks a lot for your prompt replies. Best, Alan On 25 August 2010 16:06, Berk Hess g...@hotmail.com wrote: Hi, This is completely unrelated. Eric changed all the names to allow processing of his ports by Gromacs version 3.3 and 4.0. In 4.5 I enabled fully rtp name flexibility and I changed all rtp names back to the Amber nomenclature. Berk -- From: alanwil...@gmail.com Date: Wed, 25 Aug 2010 15:39:13 +0100 Subject: Re: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now To: gmx-users@gromacs.org Not really, I mentioned that based on Sorin's ffamber page: a) Non-terminal amino and nucleic acid residues follow standard AMBER naming conventions. To avoid confusion between GROMACS and AMBER conventions, we have omitted the redundant HIS residue, leaving HID, HIE, HIP, and terminal versions of these topologies. Additionally, due to the automated changing of certain residue names by pdb2gmx, the LYS and CYS residues have been renamed LYP (Lysine plus) and CYN (Cysteine neutral, compared to AMBER residue CYM = Cysteine minus). (b) C- and N-terminal amino acids include a C or N prefix respectively, so C-terminal ALA is CALA and N-ternimal PHE is NPHE. As with non-terminal versions, the LYS and CYS terminal residues are listed as NLYP,CLYP and NCYN,CCYN. And I did mistake, it's not CYP, but CYN. So I don't know if you are fully following Sorin's recommendations. On 25 August 2010 14:36, Berk Hess g...@hotmail.com wrote: You can find the residue name to rtp translation table in: share/top/amber99.ff/aminoacids.r2b I don't have a list with Amber names and funtions for the amino acids. Currently for Amber in Gromacs we have CYS (standard, neutral, protonated) and CYX (disulfide bond). Does Amber use CYP instead of CYS? Berk -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] gmx 4.5 and openmm on Mac, still not compiling
Hi there, I've tried before and the error still basically the same (line error in 'nb_kernel400_x86_64_sse.c' was 630, now's 629) . I am using gmx 4.5 release-4-5-patches branch. git pull rm -fr build mkdir -p build cd build cmake -D BUILD_SHARED_LIBS=ON -DGMX_OPENMM=OFF .. make clean make -j 2 sudo make install # all fine till here make clean export OPENMM_ROOT_DIR=/usr/local/openmm cmake -D BUILD_SHARED_LIBS=OFF -DGMX_OPENMM=ON .. make mdrun [snip] [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/version.c.o [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c.o /Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c: In function ‘nb_kernel400nf_x86_64_sse’: /Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629: error: ‘gmx_invsqrt_exptab’ undeclared (first use in this function) /Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629: error: (Each undeclared identifier is reported only once /Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629: error: for each function it appears in.) /Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629: error: ‘gmx_invsqrt_fracttab’ undeclared (first use in this function) make[3]: *** [src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c.o] Error 1 make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2 make: *** [mdrun] Error 2 Any help would be appreciated. Thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] help with git
Hi there, I want to change from release-4-5-patches to master I am trying: git reset master git checkout master git pull error: Your local changes to 'include/resall.h' would be overwritten by merge. Aborting. Please, commit your changes or stash them before you can merge. git stash Saved working directory and index state WIP on master: 5e3473a Merge branch 'release-4-5-patches' HEAD is now at 5e3473a Merge branch 'release-4-5-patches' But I don't want branch 'release-4-5-patches'! Indeed, I am finding git very annoying to use. All I wanted in svn lingo is to change to a branch and if there's conflict, ignore all changes in my side and revert any modification to what's in the repository. Is it possible with git? Thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] help with git
Thanks Carsten, but now nothing is not working, not even what was doing so: git reset --hard HEAD is now at 5e3473a Merge branch 'release-4-5-patches' amadeus[2216]:~/workspace/gromacs% git checkout release-4-5-patches Already on 'release-4-5-patches' Your branch and 'origin/release-4-5-patches' have diverged, and have 37 and 31 different commit(s) each, respectively. amadeus[2217]:~/workspace/gromacs% git pull Auto-merging include/physics.h Auto-merging include/resall.h CONFLICT (content): Merge conflict in include/resall.h Auto-merging include/string2.h CONFLICT (content): Merge conflict in include/string2.h Auto-merging include/vec.h CONFLICT (content): Merge conflict in include/vec.h Auto-merging src/gmxlib/string2.c Auto-merging src/kernel/gen_vsite.c Auto-merging src/kernel/pdb2gmx.c Auto-merging src/kernel/pdb2top.c CONFLICT (content): Merge conflict in src/kernel/pdb2top.c Auto-merging src/kernel/resall.c Auto-merging src/kernel/ter_db.c Auto-merging src/tools/gmx_membed.c Automatic merge failed; fix conflicts and then commit the result. amadeus[2218]:~/workspace/gromacs% On 24 August 2010 12:10, Carsten Kutzner ckut...@gwdg.de wrote: On Aug 24, 2010, at 12:57 PM, Alan wrote: Hi there, I want to change from release-4-5-patches to master I am trying: git reset master git checkout master git pull error: Your local changes to 'include/resall.h' would be overwritten by merge. Aborting. Please, commit your changes or stash them before you can merge. git stash Saved working directory and index state WIP on master: 5e3473a Merge branch 'release-4-5-patches' HEAD is now at 5e3473a Merge branch 'release-4-5-patches' But I don't want branch 'release-4-5-patches'! Indeed, I am finding git very annoying to use. All I wanted in svn lingo is to change to a branch and if there's conflict, ignore all changes in my side and revert any modification to what's in the repository. git reset --hard will remove all your modifications to that branch that are not checked in yet. You might want to save include/resall.h elsewhere if you still need your modifications. Then git checkout master will check out the master branch. You might need to git pull after you checked out the master so that you are up-to-date with the gromacs repository. Carsten Is it possible with git? Thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] help with git
Ok, doing: git reset origin/release-4-5-patches git checkout origin/release-4-5-patches git pull Already up-to-date. restored the sanity of system. On 24 August 2010 13:52, Alan alanwil...@gmail.com wrote: Thanks Carsten, but now nothing is not working, not even what was doing so: git reset --hard HEAD is now at 5e3473a Merge branch 'release-4-5-patches' amadeus[2216]:~/workspace/gromacs% git checkout release-4-5-patches Already on 'release-4-5-patches' Your branch and 'origin/release-4-5-patches' have diverged, and have 37 and 31 different commit(s) each, respectively. amadeus[2217]:~/workspace/gromacs% git pull Auto-merging include/physics.h Auto-merging include/resall.h CONFLICT (content): Merge conflict in include/resall.h Auto-merging include/string2.h CONFLICT (content): Merge conflict in include/string2.h Auto-merging include/vec.h CONFLICT (content): Merge conflict in include/vec.h Auto-merging src/gmxlib/string2.c Auto-merging src/kernel/gen_vsite.c Auto-merging src/kernel/pdb2gmx.c Auto-merging src/kernel/pdb2top.c CONFLICT (content): Merge conflict in src/kernel/pdb2top.c Auto-merging src/kernel/resall.c Auto-merging src/kernel/ter_db.c Auto-merging src/tools/gmx_membed.c Automatic merge failed; fix conflicts and then commit the result. amadeus[2218]:~/workspace/gromacs% On 24 August 2010 12:10, Carsten Kutzner ckut...@gwdg.de wrote: On Aug 24, 2010, at 12:57 PM, Alan wrote: Hi there, I want to change from release-4-5-patches to master I am trying: git reset master git checkout master git pull error: Your local changes to 'include/resall.h' would be overwritten by merge. Aborting. Please, commit your changes or stash them before you can merge. git stash Saved working directory and index state WIP on master: 5e3473a Merge branch 'release-4-5-patches' HEAD is now at 5e3473a Merge branch 'release-4-5-patches' But I don't want branch 'release-4-5-patches'! Indeed, I am finding git very annoying to use. All I wanted in svn lingo is to change to a branch and if there's conflict, ignore all changes in my side and revert any modification to what's in the repository. git reset --hard will remove all your modifications to that branch that are not checked in yet. You might want to save include/resall.h elsewhere if you still need your modifications. Then git checkout master will check out the master branch. You might need to git pull after you checked out the master so that you are up-to-date with the gromacs repository. Carsten Is it possible with git? Thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] issue with pdb2gmx 4.5 and HISE oplsaa
Thanks Berk, it seems to be working now. Alan On 24 August 2010 08:54, Berk Hess g...@hotmail.com wrote: Hi, This was due to two simultaneous issues. I fixed them both for the next beta release. Note that using HIS iso HISE as a residue name would solve the problem. For 4.5 this should be the normal input, since residue names from the pdb are now preserved. Berk -- From: alanwil...@gmail.com Date: Mon, 23 Aug 2010 17:45:03 +0100 To: gmx-users@gromacs.org Subject: [gmx-users] issue with pdb2gmx 4.5 and HISE oplsaa Hi there, I have a system with 'HISE' and using gmx 4.5. ATOM 20 N HISE2 6.376 3.718 -0.053 1.00 0.00 N ATOM 21 H HISE2 5.980 4.646 -0.135 1.00 0.00 H ATOM 22 CA HISE2 7.843 3.744 -0.109 1.00 0.00 C ATOM 23 HA HISE2 8.260 3.319 0.806 1.00 0.00 H ATOM 24 CB HISE2 8.319 2.925 -1.327 1.00 0.00 C ATOM 25 HB2 HISE2 7.855 1.940 -1.312 1.00 0.00 H ATOM 26 HB1 HISE2 7.985 3.435 -2.233 1.00 0.00 H ATOM 27 CG HISE2 9.807 2.703 -1.450 1.00 0.00 C ATOM 28 ND1 HISE2 10.461 2.463 -2.655 1.00 0.00 N ATOM 29 CE1 HISE2 11.770 2.542 -2.382 1.00 0.00 C ATOM 30 HE1 HISE2 12.557 2.484 -3.124 1.00 0.00 H ATOM 31 NE2 HISE2 11.969 2.794 -1.078 1.00 0.00 N ATOM 32 HE2 HISE2 12.817 3.173 -0.672 1.00 0.00 H ATOM 33 CD2 HISE2 10.740 2.839 -0.459 1.00 0.00 C ATOM 34 HD2 HISE2 10.579 3.098 0.574 1.00 0.00 H ATOM 35 C HISE2 8.279 5.228 -0.214 1.00 0.00 C ATOM 36 O HISE2 7.440 6.079 -0.525 1.00 0.00 O when trying: pdb2gmx -f oHHH.pdb -o ogHHH.pdb -p ogHHH.top -ff oplsaa -water none Identified residue HISE1 as a starting terminus. Identified residue HISE3 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HISE1 HISE2 NE214 NE231 HISE2 NE231 0.854 HISE3 NE248 0.751 0.847 Start terminus: NH3+ End terminus: COO- --- Program pdb2gmx, VERSION 4.5-beta3-dev-20100812-97d39 Source code file: /Users/alan/Programmes/gromacs/src/kernel/pdb2gmx.c, line: 583 Fatal error: Atom HE2 in residue HISE 1 not found in rtp entry HIS1 with 19 atoms while sorting atoms. Maybe different protonation state. Remove this hydrogen or choose a different protonation state. Option -ignh will ignore all hydrogens in the input. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Why error is referencing to HIS1 (= HISA = HISD in OPLS terminology, hence != HISE) Many thanks in advance, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 http://www.bio.cam.ac.uk/%7Eawd28 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] help with git
Sorry if confused... because I am *really* confused too with git. Anyway, I started anew again and it seems to be working now. So I clone gmx: git clone git://git.gromacs.org/gromacs.git cd gromacs git branch * master git pull Already up-to-date. # now I want to move to 'release-4-5-patch' branch git checkout -t origin/release-4-5-patches Branch release-4-5-patches set up to track remote branch release-4-5-patches from origin. Switched to a new branch 'release-4-5-patches' git branch master * release-4-5-patches git pull Already up-to-date. # now I want to go back to master git checkout -t origin/master fatal: git checkout: branch master already exists git branch master * release-4-5-patches # didn't change, let's try another command (and here starts my 'guessing' experiment) git checkout master Switched to branch 'master' # nice it works! Thanks, Alan On 24 August 2010 14:14, Roland Schulz rol...@utk.edu wrote: On Tue, Aug 24, 2010 at 9:01 AM, Alan alanwil...@gmail.com wrote: Ok, doing: git reset origin/release-4-5-patches git checkout origin/release-4-5-patches I'm confused what you are trying to do. But you are not supposed to checkout a remote branch. git pull Already up-to-date. restored the sanity of system. On 24 August 2010 13:52, Alan alanwil...@gmail.com wrote: Thanks Carsten, but now nothing is not working, not even what was doing so: git reset --hard HEAD is now at 5e3473a Merge branch 'release-4-5-patches' amadeus[2216]:~/workspace/gromacs% git checkout release-4-5-patches Already on 'release-4-5-patches' Your branch and 'origin/release-4-5-patches' have diverged, and have 37 and 31 different commit(s) each, respectively. amadeus[2217]:~/workspace/gromacs% git pull Auto-merging include/physics.h Auto-merging include/resall.h CONFLICT (content): Merge conflict in include/resall.h Auto-merging include/string2.h CONFLICT (content): Merge conflict in include/string2.h Auto-merging include/vec.h CONFLICT (content): Merge conflict in include/vec.h Auto-merging src/gmxlib/string2.c Auto-merging src/kernel/gen_vsite.c Auto-merging src/kernel/pdb2gmx.c Auto-merging src/kernel/pdb2top.c CONFLICT (content): Merge conflict in src/kernel/pdb2top.c Auto-merging src/kernel/resall.c Auto-merging src/kernel/ter_db.c Auto-merging src/tools/gmx_membed.c Automatic merge failed; fix conflicts and then commit the result. amadeus[2218]:~/workspace/gromacs% On 24 August 2010 12:10, Carsten Kutzner ckut...@gwdg.de wrote: On Aug 24, 2010, at 12:57 PM, Alan wrote: Hi there, I want to change from release-4-5-patches to master I am trying: git reset master git checkout master git pull error: Your local changes to 'include/resall.h' would be overwritten by merge. Aborting. Please, commit your changes or stash them before you can merge. git stash Saved working directory and index state WIP on master: 5e3473a Merge branch 'release-4-5-patches' HEAD is now at 5e3473a Merge branch 'release-4-5-patches' But I don't want branch 'release-4-5-patches'! Indeed, I am finding git very annoying to use. All I wanted in svn lingo is to change to a branch and if there's conflict, ignore all changes in my side and revert any modification to what's in the repository. git reset --hard will remove all your modifications to that branch that are not checked in yet. You might want to save include/resall.h elsewhere if you still need your modifications. Then git checkout master will check out the master branch. You might need to git pull after you checked out the master so that you are up-to-date with the gromacs repository. Carsten Is it possible with git? Thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department
[gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now
Hi there, in special Berk. So pdb2gmx may be working with HIS and variants for oplsaa but now, something that was working before is failing: wget -c http://www.pdbe.org/download/1BNA; -O 1BNA.pdb grep 'ATOM ' 1BNA.pdb | DNA.pdb cat EOF | SPE.mdp define = -DFLEXIBLE integrator = md nsteps = 0 dt = 0.001 constraints = none emtol= 10.0 emstep = 0.01 nstcomm = 1 ns_type = simple nstlist = 0 rlist= 0 rcoulomb = 0 rvdw = 0 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 1 pbc = no nstlog = 1 nstenergy = 1 nstvout = 1 nstfout = 1 nstxtcout = 1 comm_mode = ANGULAR continuation = yes EOF pdb2gmx -f DNA.pdb -o DnaAmberSBGMX45.pdb -ff amber99sb -water none -p DnaAmberSBGMX45 [snip] 8 out of 8 lines of specbond.dat converted successfully [1]42209 segmentation fault pdb2gmx -f DNA.pdb -o DnaAmberSBGMX45.pdb -ff amber99sb -water none -p with 5e347 it worded fine, i.e, it opens files Opening force field file /Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/aminoacids.arn Opening force field file /Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/dna.arn Opening force field file /Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/rna.arn and proceed. Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now
I am using gmx 4.5 d748b. Thanks Berk, it seems to be working ... for DNA. But this one is broken (and it was working before): HHH is tripetide Hie-Hie-Hie. pdb2gmx -f HHH.pdb -o agHHH.pdb -p agHHH.top -ff amber99sb -water none [snip] Identified residue HIE1 as a starting terminus. Identified residue HIE3 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully --- Program pdb2gmx, VERSION 4.5-beta3-dev-20100824-d748b Source code file: /Users/alan/workspace/gromacs/src/kernel/pdb2top.c, line: 916 Fatal error: There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Alan On 24 August 2010 15:30, Berk Hess g...@hotmail.com wrote: Hi, I fixed it. Thanks for the fast test and the complete instructions, Berk -- From: alanwil...@gmail.com Date: Tue, 24 Aug 2010 15:22:34 +0100 To: gmx-users@gromacs.org Subject: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now Hi there, in special Berk. So pdb2gmx may be working with HIS and variants for oplsaa but now, something that was working before is failing: wget -c http://www.pdbe.org/download/1BNA; -O 1BNA.pdb grep 'ATOM ' 1BNA.pdb | DNA.pdb cat EOF | SPE.mdp define = -DFLEXIBLE integrator = md nsteps = 0 dt = 0.001 constraints = none emtol= 10.0 emstep = 0.01 nstcomm = 1 ns_type = simple nstlist = 0 rlist= 0 rcoulomb = 0 rvdw = 0 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 1 pbc = no nstlog = 1 nstenergy = 1 nstvout = 1 nstfout = 1 nstxtcout = 1 comm_mode = ANGULAR continuation = yes EOF pdb2gmx -f DNA.pdb -o DnaAmberSBGMX45.pdb -ff amber99sb -water none -p DnaAmberSBGMX45 [snip] 8 out of 8 lines of specbond.dat converted successfully [1]42209 segmentation fault pdb2gmx -f DNA.pdb -o DnaAmberSBGMX45.pdb -ff amber99sb -water none -p with 5e347 it worded fine, i.e, it opens files Opening force field file /Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/aminoacids.arn Opening force field file /Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/dna.arn Opening force field file /Volumes/CloneAmadeus/usr/local/share/gromacs/top/amber99sb.ff/rna.arn and proceed. Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 http://www.bio.cam.ac.uk/%7Eawd28 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now
Dear Berk, I understand your point and this can be very confusing. I am aware that I could use HIS and then pdb2gmx ... -his (option 1), but this is not working either with rev. d6298. Error: [snip] Which HISTIDINE type do you want for residue 3 0. H on ND1 only (HID) 1. H on NE2 only (HIE) 2. H on ND1 and NE2 (HIP) 3. Coupled to Heme (HIS1) Type a number:1 Identified residue HIS1 as a starting terminus. Identified residue HIS3 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS1HIS2 NE214 NE231 HIS2 NE231 0.854 HIS3 NE248 0.751 0.847 --- Program pdb2gmx, VERSION 4.5-beta3-dev-20100824-d6298 Source code file: /Users/alan/workspace/gromacs/src/kernel/resall.c, line: 552 Fatal error: Residue 'HISE' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors The pdb I am using is hhh.pdb ATOM 1 N HIS 1 3.389 1.609 -0.001 1.00 0.00 N ATOM 2 H1 HIS 1 4.107 0.893 -0.048 1.00 0.00 H ATOM 3 H2 HIS 1 2.795 1.549 -0.816 1.00 0.00 H ATOM 4 H3 HIS 1 2.844 1.452 0.836 1.00 0.00 H ATOM 5 CA HIS 1 4.058 2.928 0.075 1.00 0.00 C ATOM 6 HA HIS 1 3.894 3.469 -0.857 1.00 0.00 H ATOM 7 CB HIS 1 3.469 3.750 1.230 1.00 0.00 C ATOM 8 HB2 HIS 1 2.384 3.783 1.126 1.00 0.00 H ATOM 9 HB3 HIS 1 3.695 3.231 2.164 1.00 0.00 H ATOM 10 CG HIS 1 3.956 5.172 1.373 1.00 0.00 C ATOM 11 ND1 HIS 1 4.013 5.834 2.591 1.00 0.00 N ATOM 12 CE1 HIS 1 4.604 7.011 2.356 1.00 0.00 C ATOM 13 HE1 HIS 1 4.832 7.752 3.115 1.00 0.00 H ATOM 14 NE2 HIS 1 4.919 7.122 1.056 1.00 0.00 N ATOM 15 HE2 HIS 1 5.505 7.845 0.657 1.00 0.00 H ATOM 16 CD2 HIS 1 4.479 5.987 0.403 1.00 0.00 C ATOM 17 HD2 HIS 1 4.620 5.781 -0.645 1.00 0.00 H ATOM 18 C HIS 1 5.564 2.693 0.196 1.00 0.00 C ATOM 19 O HIS 1 5.947 1.551 0.422 1.00 0.00 O ATOM 20 N HIS 2 6.376 3.718 -0.053 1.00 0.00 N ATOM 21 H HIS 2 5.980 4.646 -0.135 1.00 0.00 H ATOM 22 CA HIS 2 7.843 3.744 -0.109 1.00 0.00 C ATOM 23 HA HIS 2 8.260 3.319 0.806 1.00 0.00 H ATOM 24 CB HIS 2 8.319 2.925 -1.327 1.00 0.00 C ATOM 25 HB2 HIS 2 7.855 1.940 -1.312 1.00 0.00 H ATOM 26 HB3 HIS 2 7.985 3.435 -2.233 1.00 0.00 H ATOM 27 CG HIS 2 9.807 2.703 -1.450 1.00 0.00 C ATOM 28 ND1 HIS 2 10.461 2.463 -2.655 1.00 0.00 N ATOM 29 CE1 HIS 2 11.770 2.542 -2.382 1.00 0.00 C ATOM 30 HE1 HIS 2 12.557 2.484 -3.124 1.00 0.00 H ATOM 31 NE2 HIS 2 11.969 2.794 -1.078 1.00 0.00 N ATOM 32 HE2 HIS 2 12.817 3.173 -0.672 1.00 0.00 H ATOM 33 CD2 HIS 2 10.740 2.839 -0.459 1.00 0.00 C ATOM 34 HD2 HIS 2 10.579 3.098 0.574 1.00 0.00 H ATOM 35 C HIS 2 8.279 5.228 -0.214 1.00 0.00 C ATOM 36 O HIS 2 7.440 6.079 -0.525 1.00 0.00 O ATOM 37 N HIS 3 9.547 5.520 0.075 1.00 0.00 N ATOM 38 H HIS 3 10.192 4.759 0.245 1.00 0.00 H ATOM 39 CA HIS 3 10.254 6.807 0.049 1.00 0.00 C ATOM 40 HA HIS 3 10.021 7.358 -0.860 1.00 0.00 H ATOM 41 CB HIS 3 9.841 7.621 1.297 1.00 0.00 C ATOM 42 HB2 HIS 3 8.754 7.687 1.320 1.00 0.00 H ATOM 43 HB3 HIS 3 10.158 7.074 2.185 1.00 0.00 H ATOM 44 CG HIS 3 10.359 9.037 1.429 1.00 0.00 C ATOM 45 ND1 HIS 3 10.137 9.848 2.546 1.00 0.00 N ATOM 46 CE1 HIS 3 10.788 10.994 2.308 1.00 0.00 C ATOM 47 HE1 HIS 3 10.849 11.818 3.006 1.00 0.00 H ATOM 48 NE2 HIS 3 11.375 10.962 1.100 1.00 0.00 N ATOM 49 HE2 HIS 3 11.977 11.674 0.715 1.00 0.00 H ATOM 50 CD2 HIS 3 11.100 9.742 0.525 1.00 0.00 C ATOM 51 HD2 HIS 3 11.456 9.376 -0.428 1.00 0.00 H ATOM 52 C HIS 3 11.761 6.487 0.002 1.00 0.00 C ATOM 53 O HIS 3 12.128 5.407 0.518 1.00 0.00 O ATOM 54 OXT HIS 3 12.494 7.275 -0.632 1.00 0.00 O Now, using HIE (HHH.pdb, like hhh.pdb but HIE for res instead of HIS) with export GMX_FFRTP_TER_RENAME=1 and then pdb2gmx -f HHH.pdb -o HHH.pdb -p agHHH.top -ff amber99sb -water none
[gmx-users] issue with pdb2gmx 4.5 and HISE oplsaa
Hi there, I have a system with 'HISE' and using gmx 4.5. ATOM 20 N HISE2 6.376 3.718 -0.053 1.00 0.00 N ATOM 21 H HISE2 5.980 4.646 -0.135 1.00 0.00 H ATOM 22 CA HISE2 7.843 3.744 -0.109 1.00 0.00 C ATOM 23 HA HISE2 8.260 3.319 0.806 1.00 0.00 H ATOM 24 CB HISE2 8.319 2.925 -1.327 1.00 0.00 C ATOM 25 HB2 HISE2 7.855 1.940 -1.312 1.00 0.00 H ATOM 26 HB1 HISE2 7.985 3.435 -2.233 1.00 0.00 H ATOM 27 CG HISE2 9.807 2.703 -1.450 1.00 0.00 C ATOM 28 ND1 HISE2 10.461 2.463 -2.655 1.00 0.00 N ATOM 29 CE1 HISE2 11.770 2.542 -2.382 1.00 0.00 C ATOM 30 HE1 HISE2 12.557 2.484 -3.124 1.00 0.00 H ATOM 31 NE2 HISE2 11.969 2.794 -1.078 1.00 0.00 N ATOM 32 HE2 HISE2 12.817 3.173 -0.672 1.00 0.00 H ATOM 33 CD2 HISE2 10.740 2.839 -0.459 1.00 0.00 C ATOM 34 HD2 HISE2 10.579 3.098 0.574 1.00 0.00 H ATOM 35 C HISE2 8.279 5.228 -0.214 1.00 0.00 C ATOM 36 O HISE2 7.440 6.079 -0.525 1.00 0.00 O when trying: pdb2gmx -f oHHH.pdb -o ogHHH.pdb -p ogHHH.top -ff oplsaa -water none Identified residue HISE1 as a starting terminus. Identified residue HISE3 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HISE1 HISE2 NE214 NE231 HISE2 NE231 0.854 HISE3 NE248 0.751 0.847 Start terminus: NH3+ End terminus: COO- --- Program pdb2gmx, VERSION 4.5-beta3-dev-20100812-97d39 Source code file: /Users/alan/Programmes/gromacs/src/kernel/pdb2gmx.c, line: 583 Fatal error: Atom HE2 in residue HISE 1 not found in rtp entry HIS1 with 19 atoms while sorting atoms. Maybe different protonation state. Remove this hydrogen or choose a different protonation state. Option -ignh will ignore all hydrogens in the input. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Why error is referencing to HIS1 (= HISA = HISD in OPLS terminology, hence != HISE) Many thanks in advance, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] please, how edr data is xdr packed?
Hi there, I am trying to use python xdrlib module to read edr files but not knowing how the data is packed using the xdr protocol makes my work very difficult, if not impossible. Would someone kindly tell me how data is packed in the edr file? Or where it is the gromacs code so I can try to figure out a way? I've read http://tools.ietf.org/html/rfc1832.html and for reference, see topic 6. AN EXAMPLE OF AN XDR DATA DESCRIPTION. My other option would be using a parsing code to read g_energy output but this seems very silly. Many thanks in advance, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: dihedraltypes funct 4 and 9 in gmx 4.5 amber
Hi there,
Now I have some results that I hope to clear this matter about dihe funct 4
and 9 (specially the latter).
Please see:
http://code.google.com/p/acpype/wiki/TestingAcpypeAmb2gmx
From my understanding (and results), where dihe funct 4 or 9, replacing both
with 1 changes nothing in tot pot energy for amber force fields.
I don't know about charmm here, but I thought amber dihe parameters were
sort multiple terms and as far as I remember, the need to convert proper
dihe to RBs was necessary for early versions of gromacs 3.x, am I right?
Best,
Alan
On 18 August 2010 22:01, Alan alanwil...@gmail.com wrote:
Hi Berk and Mark,
Erik was too lazy to document this, I now added it to the manual.
Is this manual available even via git? When funct 4 and 9 appeared? in gmx
4.5?
Type 4 is identical to type 1, it is only there to distinguish improper
from proper dihedrals.
So for amber impr. dih. only, if I put 1 instead of 4 I for my GAFF
generated ligand it would do the same thing, right? I ask that for the grace
of compatibility with gmx 4.0.x.
Type 9 is identical to type 1, except that multiple entries in
dihedraltypes will lead to
multiple functions on one dihedral.
This one is more difficult to get. I know about multiple entries in CNS,
Charmm and Amber. I was even trying to convert amber99bsc0 new dih
parameters to gromacs and I was using funct 1. However I didn't have Amber
to validate, and now I have Amber11, I don't have time for the moment.
Sounds like funct 9 is to not only pave the way for Charmm, but may help to
address properly the bsc0 parameters, right?
But I need to understand this better. Converting amber's proper dih. param.
to gromacs 4.0.x was done by making these dih. to be RB. However
amb2gmx.pl converts everything to proper (using funct 1) -- acpype is
smarter here. So in gmx 4.0.x proper dih. funct 1 was never able to
interpret multiple entries on one dihedral?
Now on Mark:
Type 9 was added to facilitate CHARMM's multiple proper dihedrals, in git
commit a7c597c778351f by Erik, whose message was
Added support for dihedraltype 9, which allows multiple terms for
proper dihedrals.
By listing a dihedral with type 9, grompp will now scan the force field
to see if there are
multiple terms on _adjacent_ lines listed in the dihedraltypes section,
and in that case add them all.
A code snippet in src/kernel/toppush.c reads
if(ft == 9)
{
/* Previously, we have always overwritten parameters if
e.g. a torsion
with the same atomtypes occurs on multiple lines. However,
CHARMM and
some other force fields specify multiple dihedrals over
some bonds,
including cosines with multiplicity 6 and somethimes even
higher.
Thus, they cannot be represented with Ryckaert-Bellemans
terms.
To add support for these force fields, Dihedral type 9 is
identical to
normal proper dihedrals, but repeated entries are allowed.
*/
bAllowRepeat = TRUE;
ft = 1;
}
So amb2gmx.pl never worked properly here? For example, I have this for DNA
with amber99bsc0:
; treated as usual propers in GROMACS since Phase angle diff from 0 or 180
degrees
; i j k l func phase kd pn
2 3 6 23 1 190.98 4.92892 1 ;O5'- C5'- C4'- C3'
2 3 6 23 1 295.63 0.38535 2 ;O5'- C5'- C4'- C3'
2 3 6 23 1 348.10 4.02848 3 ;O5'- C5'- C4'- C3'
28 29 32 33 131.80 0.77480 1 ;O3'- P- O5'- C5'
28 29 32 33 1 351.96 5.25733 2 ;O3'- P- O5'- C5'
28 29 32 33 1 357.25 1.48473 3 ;O3'- P- O5'- C5'
So, this would only work if funct was 9 and not 1 as above? The way it is,
the last line of a sequence dih. is overwriting the 2 previous one, ignoring
them completely?
From src/gmxlib/{ifunc,bondfree}.c and src/kernel/{topdirs,toppush}.c it
can be seen that dihedraltypes 4 and 1 call the same evaluation function.
Perhaps Erik can confirm this.
src/gmxlib/ifunc.c did suggest to me that something is not quite right...
def_bonded (PDIHS,Proper Dih., 4, 3, 3, eNR_PROPER, pdihs
),
def_bonded (RBDIHS, Ryckaert-Bell., 4, 6, 6, eNR_RB, rbdihs
),
def_bonded (FOURDIHS, Fourier Dih.,4, 4, 4, eNR_FOURDIH, rbdihs
),
def_bonded (IDIHS,Improper Dih., 4, 2, 2, eNR_IMPROPER,idihs
),
def_bonded (PIDIHS, Improper Dih., 4, 3, 3, eNR_PROPER, pdihs
),
If PIDIHS is an improper dihedral with the functional form of a proper
dihedral, should it not use eNR_IMPROPER?
I definitely need to run my validations myself, but any words here would be
helpful.
Many thanks you all.
Cheers,
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry
[gmx-users] Re: dihedraltypes funct 4 and 9 in gmx 4.5 amber
Ah! now I get it. Thanks Berk. On 20 August 2010 16:27, gmx-users-requ...@gromacs.org wrote: Hi, That depends. If you have explicit parameters in the dihedral section then 1 and 9 are equivalent. If grompp has to look up parameters in the dihderaltypes section there will be difference when multiple parameter lines are present the same atom types for a dihedral type 9. Berk -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] help to parse edr file using xdrlib in python
Hi there,
I am trying to retrieve energies calculated by gmx in python code. It sounds
that I could use xdrlib if only I could understand how gmx data were packed
in the edr file.
For example, I am doing this:
import xdrlib
In: f = open('aogAAA.edr').read()
In: data = xdrlib.Unpacker(f)
In: repr(data.unpack_string())
Out:
'\\x00\\x00\\x00\\x04Bond\\x00\\x00\\x00\\x05Angle\\x00\\x00\\x00\\x00\\x00\\x00\\x0bProper
Dih.\\x00'
# what?
In: repr(data.unpack_string())
Out: 'Ryckaert-Bell.'
# hum, sounds better, but to get the type of data associated?
# a guess
In: data.unpack_float()
Out: 5.605193857299268e-45
# Ok, what that means?
Any help here would be appreciated.
Many thanks,
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
http://www.bio.cam.ac.uk/~awd28
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: dihedraltypes funct 4 and 9 in gmx 4.5 amber
Hi Berk and Mark,
Erik was too lazy to document this, I now added it to the manual.
Is this manual available even via git? When funct 4 and 9 appeared? in gmx
4.5?
Type 4 is identical to type 1, it is only there to distinguish improper from
proper dihedrals.
So for amber impr. dih. only, if I put 1 instead of 4 I for my GAFF
generated ligand it would do the same thing, right? I ask that for the grace
of compatibility with gmx 4.0.x.
Type 9 is identical to type 1, except that multiple entries in dihedraltypes
will lead to
multiple functions on one dihedral.
This one is more difficult to get. I know about multiple entries in CNS,
Charmm and Amber. I was even trying to convert amber99bsc0 new dih
parameters to gromacs and I was using funct 1. However I didn't have Amber
to validate, and now I have Amber11, I don't have time for the moment.
Sounds like funct 9 is to not only pave the way for Charmm, but may help to
address properly the bsc0 parameters, right?
But I need to understand this better. Converting amber's proper dih. param.
to gromacs 4.0.x was done by making these dih. to be RB. However
amb2gmx.plconverts everything to proper (using funct 1) -- acpype is
smarter here. So
in gmx 4.0.x proper dih. funct 1 was never able to interpret multiple
entries on one dihedral?
Now on Mark:
Type 9 was added to facilitate CHARMM's multiple proper dihedrals, in git
commit a7c597c778351f by Erik, whose message was
Added support for dihedraltype 9, which allows multiple terms for proper
dihedrals.
By listing a dihedral with type 9, grompp will now scan the force field
to see if there are
multiple terms on _adjacent_ lines listed in the dihedraltypes section,
and in that case add them all.
A code snippet in src/kernel/toppush.c reads
if(ft == 9)
{
/* Previously, we have always overwritten parameters if e.g.
a torsion
with the same atomtypes occurs on multiple lines. However,
CHARMM and
some other force fields specify multiple dihedrals over
some bonds,
including cosines with multiplicity 6 and somethimes even
higher.
Thus, they cannot be represented with Ryckaert-Bellemans
terms.
To add support for these force fields, Dihedral type 9 is
identical to
normal proper dihedrals, but repeated entries are allowed.
*/
bAllowRepeat = TRUE;
ft = 1;
}
So amb2gmx.pl never worked properly here? For example, I have this for DNA
with amber99bsc0:
; treated as usual propers in GROMACS since Phase angle diff from 0 or 180
degrees
; i j k l func phase kd pn
2 3 6 23 1 190.98 4.92892 1 ;O5'- C5'- C4'- C3'
2 3 6 23 1 295.63 0.38535 2 ;O5'- C5'- C4'- C3'
2 3 6 23 1 348.10 4.02848 3 ;O5'- C5'- C4'- C3'
28 29 32 33 131.80 0.77480 1 ;O3'- P- O5'- C5'
28 29 32 33 1 351.96 5.25733 2 ;O3'- P- O5'- C5'
28 29 32 33 1 357.25 1.48473 3 ;O3'- P- O5'- C5'
So, this would only work if funct was 9 and not 1 as above? The way it is,
the last line of a sequence dih. is overwriting the 2 previous one, ignoring
them completely?
From src/gmxlib/{ifunc,bondfree}.c and src/kernel/{topdirs,toppush}.c it
can be seen that dihedraltypes 4 and 1 call the same evaluation function.
Perhaps Erik can confirm this.
src/gmxlib/ifunc.c did suggest to me that something is not quite right...
def_bonded (PDIHS,Proper Dih., 4, 3, 3, eNR_PROPER, pdihs
),
def_bonded (RBDIHS, Ryckaert-Bell., 4, 6, 6, eNR_RB, rbdihs
),
def_bonded (FOURDIHS, Fourier Dih.,4, 4, 4, eNR_FOURDIH, rbdihs
),
def_bonded (IDIHS,Improper Dih., 4, 2, 2, eNR_IMPROPER,idihs
),
def_bonded (PIDIHS, Improper Dih., 4, 3, 3, eNR_PROPER, pdihs
),
If PIDIHS is an improper dihedral with the functional form of a proper
dihedral, should it not use eNR_IMPROPER?
I definitely need to run my validations myself, but any words here would be
helpful.
Many thanks you all.
Cheers,
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
http://www.bio.cam.ac.uk/~awd28
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] dihedraltypes funct 4 and 9 in gmx 4.5 amber ff
Hi there, I've been looking at amber ff implementation of gmx 4.5 since I am familiar to Sorin's ffamber works and I am the developer of ACPYPE. I noticed that proper dih are not converted to RB anymore (which's great for understanding) and to accomplish that apparently 2 new funct were added to the gmx code, namely 4 and 9. Needless to say that I couldn't find anything about funct 4 and 9 in the current gmx manual. I would appreciate more information about it. Among other things I would like to know, e.g., what funct 4 would have different from funct 1, since in the seminal work of Sorin, amber impr. dih are treated as prop. dih in gromacs. Many thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: broken links
Thanks, it's working now. Alan On 11 August 2010 17:59, Alan alanwil...@gmail.com wrote: Hi there, I cannot download from http://www.gromacs.org/Downloads/Installation_Instructions/compiling_QMMMany file and link to Gamess-UK seems to be broken as well. Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: gromacs from git failed with cmake on Mac SL and fftw from Fink
Thanks, I saw your commits at gromacs git and cmake worked fine now. Alan On 11 August 2010 17:34, Alan alanwil...@gmail.com wrote: Hi there, I am using gromacs from git source with cmake on Mac SL with Fink. ~/Programmes/gromacs% git show commit 86226a1a075a071920b0413aa7030545f8e6e282 Merge: b8f35b9 c903375 Author: Berk Hess h...@csbl10.(none) Date: Wed Aug 11 12:57:53 2010 +0200 Merge remote branch 'origin/release-4-5-patches' If using the old way (after bootstrapping), everything goes fine with: ./configure CPPFLAGS=-I/sw/include LDFLAGS=-L/sw/lib --with-gsl --with-x With cmake (cmake -D BUILD_SHARED_LIBS=ON or OFF), although CMakeCache.txt seems to be correct, for example, I see: //Path to a file. FFTW3F_INCLUDE_DIR:PATH=/sw/include //Path to a library. FFTW3F_LIBRARIES:FILEPATH=/sw/lib/libfftw3f.dylib (But have no idea if using gsl libs) I got this error: [ skip ] Scanning dependencies of target grompp [ 77%] Building C object src/kernel/CMakeFiles/grompp.dir/grompp.c.o Linking C executable grompp [ 77%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_lie.c.o Undefined symbols: _fftwf_plan_many_dft_r2c, referenced from: _gmx_fft_init_many_1d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_many_1d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_many_1d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_many_1d_real in libmd.a(gmx_fft_fftw3.c.o) _fftwf_plan_dft_r2c_2d, referenced from: _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.c.o) _fftwf_plan_dft_r2c_3d, referenced from: _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.c.o) _fftwf_malloc, referenced from: _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_many_1d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_many_1d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_many_1d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_many_1d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_many_1d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_many_1d in libmd.a(gmx_fft_fftw3.c.o) _fftwf_execute_dft_c2r, referenced from: _gmx_fft_3d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_2d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_1d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_many_1d_real in libmd.a(gmx_fft_fftw3.c.o) _fftwf_free, referenced from: _gmx_fft_destroy in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_many_1d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_many_1d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_many_1d_real in libmd.a(gmx_fft_fftw3.c.o
[gmx-users] gromacs from git source and openmm failed
Hi there, I am trying now to compile mdrun-openmm, by doing: cmake -DGMX_OPENMM=ON .. make mdrun -- Threads not compatible with OpenMM build, disabled CMake Warning at CMakeLists.txt:127 (message): The OpenMM build does not support other acceleration modes! -- Using internal FFT library - fftpack -- Loaded CMakeASM-ATTInformation - ASM-ATT support is still experimental, please report issues -- Configuring done -- Generating done -- Build files have been written to: /Users/alan/Programmes/gromacs/build dhcp-128-232-144-215[2416]:~/Programmes/gromacs/build% make mdrun [ 0%] Building NVCC (Device) object src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_memtestG80_core.cu.o [ 1%] Building NVCC (Device) object src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_gmx_gpu_utils.cu.o ... And then I got this error: ... [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c.o /Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c: In function ‘nb_kernel400nf_x86_64_sse’: /Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:630: error: ‘gmx_invsqrt_exptab’ undeclared (first use in this function) /Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:630: error: (Each undeclared identifier is reported only once /Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:630: error: for each function it appears in.) /Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:630: error: ‘gmx_invsqrt_fracttab’ undeclared (first use in this function) make[3]: *** [src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c.o] Error 1 make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2 make: *** [mdrun] Error 2 Thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: gromacs from git source and openmm failed
Thanks Rossen, Try it again with the latest release-4-5-branch, Erik added a lot of fixes. Indeed, when I did my report *was* with Erik's mods, which I am afraid, was what broke the compilation. I am using 'git log': Author: Rossen Apostolov ros...@cbr.su.se Date: Thu Aug 12 11:20:18 2010 +0200 Fixed a reverted version string in configure.ac BTW, is there simpler way to say the revision number in git like 'svn info'? Thanks Alan On 12 August 2010 12:11, Alan alanwil...@gmail.com wrote: Hi there, I am trying now to compile mdrun-openmm, by doing: cmake -DGMX_OPENMM=ON .. make mdrun -- Threads not compatible with OpenMM build, disabled CMake Warning at CMakeLists.txt:127 (message): The OpenMM build does not support other acceleration modes! -- Using internal FFT library - fftpack -- Loaded CMakeASM-ATTInformation - ASM-ATT support is still experimental, please report issues -- Configuring done -- Generating done -- Build files have been written to: /Users/alan/Programmes/gromacs/build dhcp-128-232-144-215[2416]:~/Programmes/gromacs/build% make mdrun [ 0%] Building NVCC (Device) object src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_memtestG80_core.cu.o [ 1%] Building NVCC (Device) object src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_gmx_gpu_utils.cu.o ... And then I got this error: ... [ 56%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c.o /Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c: In function ‘nb_kernel400nf_x86_64_sse’: /Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:630: error: ‘gmx_invsqrt_exptab’ undeclared (first use in this function) /Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:630: error: (Each undeclared identifier is reported only once /Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:630: error: for each function it appears in.) /Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:630: error: ‘gmx_invsqrt_fracttab’ undeclared (first use in this function) make[3]: *** [src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c.o] Error 1 make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2 make: *** [mdrun] Error 2 Thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] gromacs from git, using cmake, where's gsl option?
Hi list, I am giving a try with gromacs from git source using cmake. It seems to get everything right in my system (Mac SL 64 bits) but I have no idea if it's using gsl lib as I would do if using the old method ./configure --with-gsl etc. Can someone please make it clear here? Many thanks in advance, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] gromacs from git failed with cmake on Mac SL and fftw from Fink
(gmx_fft_fftw3.c.o) _gmx_fft_init_many_1d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_many_1d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_many_1d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_many_1d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_many_1d in libmd.a(gmx_fft_fftw3.c.o) _fftwf_execute_dft_r2c, referenced from: _gmx_fft_3d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_2d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_1d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_many_1d_real in libmd.a(gmx_fft_fftw3.c.o) _fftwf_execute, referenced from: _fft5d_execute in libmd.a(fft5d.c.o) _fft5d_execute in libmd.a(fft5d.c.o) _fftwf_plan_dft_c2r_2d, referenced from: _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_2d_real in libmd.a(gmx_fft_fftw3.c.o) _fftwf_plan_dft_c2r_3d, referenced from: _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_3d_real in libmd.a(gmx_fft_fftw3.c.o) _fftwf_destroy_plan, referenced from: _gmx_fft_destroy in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_destroy in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_destroy in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_destroy in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_destroy in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_destroy in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_destroy in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_destroy in libmd.a(gmx_fft_fftw3.c.o) _fftwf_plan_many_dft, referenced from: _gmx_fft_init_many_1d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_many_1d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_many_1d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_many_1d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_many_1d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_many_1d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_many_1d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_many_1d in libmd.a(gmx_fft_fftw3.c.o) _fftwf_plan_guru_dft, referenced from: _fft5d_plan_3d in libmd.a(fft5d.c.o) _fftwf_execute_dft, referenced from: _gmx_fft_3d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_2d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_1d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_many_1d in libmd.a(gmx_fft_fftw3.c.o) _fftwf_plan_guru_dft_c2r, referenced from: _fft5d_plan_3d in libmd.a(fft5d.c.o) _fftwf_plan_dft_2d, referenced from: _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_2d in libmd.a(gmx_fft_fftw3.c.o) _fftwf_plan_dft_3d, referenced from: _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_3d in libmd.a(gmx_fft_fftw3.c.o) _fftwf_plan_guru_dft_r2c, referenced from: _fft5d_plan_3d in libmd.a(fft5d.c.o) _fftwf_plan_many_dft_c2r, referenced from: _gmx_fft_init_many_1d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_many_1d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_many_1d_real in libmd.a(gmx_fft_fftw3.c.o) _gmx_fft_init_many_1d_real in libmd.a(gmx_fft_fftw3.c.o) ld: symbol(s) not found collect2: ld returned 1 exit status make[2]: *** [src/kernel/grompp] Error 1 make[1]: *** [src/kernel/CMakeFiles/grompp.dir/all] Error 2 make[1]: *** Waiting for unfinished jobs [ 77%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_filter.c.o [ 77%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_gyrate.c.o [ skip ] [ 85%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_membed.c.o Linking C static library libgmxana.a [ 85%] Built target gmxana make: *** [all] Error 2 Any help would be appreciated, many thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post
[gmx-users] broken links
Hi there, I cannot download from http://www.gromacs.org/Downloads/Installation_Instructions/compiling_QMMMany file and link to Gamess-UK seems to be broken as well. Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] pdb atom nomenclature in gmx rtp files
Hi there, I see in ffoplsaa.rtp that, e.g., CYS has: HB1opls_1400.060 2 HB2opls_1400.060 2 But according to latest PDB atom nomenclature it should be: HB2 ... HB3 ... Of course that using pdb2gmx -ignh and it should avoid this problem, but unless for any other specific reason, I find this quite annoying. GMX 4.5 still doesn't address this. So, is there plans to bring rtp atom nomenclature to the latest PDB standards or this task is not necessary (and I missing something else) or only in gmx 5 when pdb2gmx gets smarter? Many thanks in advance, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: gmx 4.5 issue with grompp
Thanks Roland, it did work.
Cheers,
Alan
On Sun, Aug 1, 2010 at 09:46, gmx-users-requ...@gromacs.org wrote:
Alan,
with the following change your example works for me.
diff --git a/src/gmxlib/inputrec.c b/src/gmxlib/inputrec.c
index 581ae4c..e148612 100644
--- a/src/gmxlib/inputrec.c
+++ b/src/gmxlib/inputrec.c
@@ -169,7 +169,7 @@ int ir_optimal_nstpcouple(const t_inputrec *ir)
{
int nmin,nwanted,n;
-nmin = pcouple_min_integration_steps(ir-etc);
+nmin = pcouple_min_integration_steps(ir-epc);
nwanted = nst_wanted(ir);
Or you can also update from git.
@Berk: Could you please verify that this fix is correct?
Roland
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
http://www.bio.cam.ac.uk/~awd28
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] gmx 4.5 configure options confusing
For gmx 4.5 beta, I see with ./configure --help: --without-qmmm-mopacUse modified Mopac 7 for QM-MM (see website) --without-qmmm-mopacUse ORCA for QM-MM What that really means? Thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] error compiling gmx 4.5 on Mac 10.6.4
Hi there, I am trying gmx 4.5 beta on Mac SL 10.6.4 with Fink, doing: ./configure CPPFLAGS=-I/sw/include LDFLAGS=-L/sw/lib --enable-shared --with-gsl --with-x and then 'make' failed with: (cd .libs/libgmx.lax/libthread_mpi.a ar x /Users/alan/Downloads/gromacs-4.5-beta1/src/gmxlib/thread_mpi/.libs/libthread_mpi.a) cc -dynamiclib -o .libs/libgmx.6.dylib .libs/3dview.o .libs/atomprop.o .libs/bondfree.o .libs/calcgrid.o .libs/calch.o .libs/chargegroup.o .libs/checkpoint.o .libs/confio.o .libs/copyrite.o .libs/disre.o .libs/do_fit.o .libs/enxio.o .libs/ewald_util.o .libs/ffscanf.o .libs/filenm.o .libs/futil.o .libs/gbutil.o .libs/gmx_fatal.o .libs/gmx_sort.o .libs/gmxcpp.o .libs/gmxfio.o .libs/ifunc.o .libs/index.o .libs/inputrec.o .libs/cinvsqrtdata.o .libs/invblock.o .libs/macros.o .libs/orires.o .libs/sparsematrix.o .libs/main.o .libs/maths.o .libs/matio.o .libs/mshift.o .libs/mtop_util.o .libs/mtxio.o .libs/mvdata.o .libs/names.o .libs/network.o .libs/nrama.o .libs/nrjac.o .libs/nrnb.o .libs/pargs.o .libs/pbc.o .libs/pdbio.o .libs/princ.o .libs/rando.o .libs/random.o .libs/gmx_random.o .libs/rbin.o .libs/readinp.o .libs/replace.o .libs/rmpbc.o .libs/shift_util.o .libs/sortwater.o .libs/smalloc.o .libs/statutil.o .libs/sfactor.o .libs/strdb.o .libs/string2.o .libs/symtab.o .libs/topsort.o .libs/tpxio.o .libs/trnio.o .libs/trxio.o .libs/txtdump.o .libs/typedefs.o .libs/viewit.o .libs/warninp.o .libs/wgms.o .libs/wman.o .libs/writeps.o .libs/xdrd.o .libs/xtcio.o .libs/xvgr.o .libs/libxdrf.o .libs/gmx_arpack.o .libs/gmx_matrix.o .libs/dihres.o .libs/tcontrol.o .libs/splitter.o .libs/gmx_cyclecounter.o .libs/gmx_system_xdr.o .libs/md5.o .libs/vmdio.o .libs/vmddlopen.o .libs/sighandler.o .libs/oenv.o .libs/gmxfio_rw.o .libs/gmxfio_asc.o .libs/gmxfio_bin.o .libs/gmxfio_xdr.o .libs/libgmx.lax/libnonbonded.a/nb_free_energy.o .libs/libgmx.lax/libnonbonded.a/nb_generic.o .libs/libgmx.lax/libnonbonded.a/nb_generic_cg.o .libs/libgmx.lax/libnonbonded.a/nb_kernel010.o .libs/libgmx.lax/libnonbonded.a/nb_kernel010_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel020.o .libs/libgmx.lax/libnonbonded.a/nb_kernel030.o .libs/libgmx.lax/libnonbonded.a/nb_kernel030_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel100.o .libs/libgmx.lax/libnonbonded.a/nb_kernel100_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel101.o .libs/libgmx.lax/libnonbonded.a/nb_kernel101_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel102.o .libs/libgmx.lax/libnonbonded.a/nb_kernel102_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel103.o .libs/libgmx.lax/libnonbonded.a/nb_kernel103_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel104.o .libs/libgmx.lax/libnonbonded.a/nb_kernel104_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel110.o .libs/libgmx.lax/libnonbonded.a/nb_kernel110_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel111.o .libs/libgmx.lax/libnonbonded.a/nb_kernel111_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel112.o .libs/libgmx.lax/libnonbonded.a/nb_kernel112_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel113.o .libs/libgmx.lax/libnonbonded.a/nb_kernel113_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel114.o .libs/libgmx.lax/libnonbonded.a/nb_kernel114_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel120.o .libs/libgmx.lax/libnonbonded.a/nb_kernel121.o .libs/libgmx.lax/libnonbonded.a/nb_kernel122.o .libs/libgmx.lax/libnonbonded.a/nb_kernel123.o .libs/libgmx.lax/libnonbonded.a/nb_kernel124.o .libs/libgmx.lax/libnonbonded.a/nb_kernel130.o .libs/libgmx.lax/libnonbonded.a/nb_kernel130_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel131.o .libs/libgmx.lax/libnonbonded.a/nb_kernel131_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel132.o .libs/libgmx.lax/libnonbonded.a/nb_kernel132_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel133.o .libs/libgmx.lax/libnonbonded.a/nb_kernel133_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel134.o .libs/libgmx.lax/libnonbonded.a/nb_kernel134_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel200.o .libs/libgmx.lax/libnonbonded.a/nb_kernel200_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel201.o .libs/libgmx.lax/libnonbonded.a/nb_kernel201_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel202.o .libs/libgmx.lax/libnonbonded.a/nb_kernel202_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel203.o .libs/libgmx.lax/libnonbonded.a/nb_kernel203_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel204.o .libs/libgmx.lax/libnonbonded.a/nb_kernel204_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel210.o .libs/libgmx.lax/libnonbonded.a/nb_kernel210_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel211.o .libs/libgmx.lax/libnonbonded.a/nb_kernel211_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel212.o .libs/libgmx.lax/libnonbonded.a/nb_kernel212_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel213.o .libs/libgmx.lax/libnonbonded.a/nb_kernel213_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a
[gmx-users] Re: error compiling gmx 4.5 on Mac 10.6.4
To myself. Removing --enable-shared and compilation went fine. Alan On Sat, Jul 31, 2010 at 11:41, Alan alanwil...@gmail.com wrote: Hi there, I am trying gmx 4.5 beta on Mac SL 10.6.4 with Fink, doing: ./configure CPPFLAGS=-I/sw/include LDFLAGS=-L/sw/lib --enable-shared --with-gsl --with-x and then 'make' failed with: (cd .libs/libgmx.lax/libthread_mpi.a ar x /Users/alan/Downloads/gromacs-4.5-beta1/src/gmxlib/thread_mpi/.libs/libthread_mpi.a) cc -dynamiclib -o .libs/libgmx.6.dylib .libs/3dview.o .libs/atomprop.o .libs/bondfree.o .libs/calcgrid.o .libs/calch.o .libs/chargegroup.o .libs/checkpoint.o .libs/confio.o .libs/copyrite.o .libs/disre.o .libs/do_fit.o .libs/enxio.o .libs/ewald_util.o .libs/ffscanf.o .libs/filenm.o .libs/futil.o .libs/gbutil.o .libs/gmx_fatal.o .libs/gmx_sort.o .libs/gmxcpp.o .libs/gmxfio.o .libs/ifunc.o .libs/index.o .libs/inputrec.o .libs/cinvsqrtdata.o .libs/invblock.o .libs/macros.o .libs/orires.o .libs/sparsematrix.o .libs/main.o .libs/maths.o .libs/matio.o .libs/mshift.o .libs/mtop_util.o .libs/mtxio.o .libs/mvdata.o .libs/names.o .libs/network.o .libs/nrama.o .libs/nrjac.o .libs/nrnb.o .libs/pargs.o .libs/pbc.o .libs/pdbio.o .libs/princ.o .libs/rando.o .libs/random.o .libs/gmx_random.o .libs/rbin.o .libs/readinp.o .libs/replace.o .libs/rmpbc.o .libs/shift_util.o .libs/sortwater.o .libs/smalloc.o .libs/statutil.o .libs/sfactor.o .libs/strdb.o .libs/string2.o .libs/symtab.o .libs/topsort.o .libs/tpxio.o .libs/trnio.o .libs/trxio.o .libs/txtdump.o .libs/typedefs.o .libs/viewit.o .libs/warninp.o .libs/wgms.o .libs/wman.o .libs/writeps.o .libs/xdrd.o .libs/xtcio.o .libs/xvgr.o .libs/libxdrf.o .libs/gmx_arpack.o .libs/gmx_matrix.o .libs/dihres.o .libs/tcontrol.o .libs/splitter.o .libs/gmx_cyclecounter.o .libs/gmx_system_xdr.o .libs/md5.o .libs/vmdio.o .libs/vmddlopen.o .libs/sighandler.o .libs/oenv.o .libs/gmxfio_rw.o .libs/gmxfio_asc.o .libs/gmxfio_bin.o .libs/gmxfio_xdr.o .libs/libgmx.lax/libnonbonded.a/nb_free_energy.o .libs/libgmx.lax/libnonbonded.a/nb_generic.o .libs/libgmx.lax/libnonbonded.a/nb_generic_cg.o .libs/libgmx.lax/libnonbonded.a/nb_kernel010.o .libs/libgmx.lax/libnonbonded.a/nb_kernel010_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel020.o .libs/libgmx.lax/libnonbonded.a/nb_kernel030.o .libs/libgmx.lax/libnonbonded.a/nb_kernel030_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel100.o .libs/libgmx.lax/libnonbonded.a/nb_kernel100_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel101.o .libs/libgmx.lax/libnonbonded.a/nb_kernel101_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel102.o .libs/libgmx.lax/libnonbonded.a/nb_kernel102_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel103.o .libs/libgmx.lax/libnonbonded.a/nb_kernel103_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel104.o .libs/libgmx.lax/libnonbonded.a/nb_kernel104_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel110.o .libs/libgmx.lax/libnonbonded.a/nb_kernel110_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel111.o .libs/libgmx.lax/libnonbonded.a/nb_kernel111_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel112.o .libs/libgmx.lax/libnonbonded.a/nb_kernel112_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel113.o .libs/libgmx.lax/libnonbonded.a/nb_kernel113_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel114.o .libs/libgmx.lax/libnonbonded.a/nb_kernel114_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel120.o .libs/libgmx.lax/libnonbonded.a/nb_kernel121.o .libs/libgmx.lax/libnonbonded.a/nb_kernel122.o .libs/libgmx.lax/libnonbonded.a/nb_kernel123.o .libs/libgmx.lax/libnonbonded.a/nb_kernel124.o .libs/libgmx.lax/libnonbonded.a/nb_kernel130.o .libs/libgmx.lax/libnonbonded.a/nb_kernel130_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel131.o .libs/libgmx.lax/libnonbonded.a/nb_kernel131_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel132.o .libs/libgmx.lax/libnonbonded.a/nb_kernel132_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel133.o .libs/libgmx.lax/libnonbonded.a/nb_kernel133_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel134.o .libs/libgmx.lax/libnonbonded.a/nb_kernel134_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel200.o .libs/libgmx.lax/libnonbonded.a/nb_kernel200_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel201.o .libs/libgmx.lax/libnonbonded.a/nb_kernel201_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel202.o .libs/libgmx.lax/libnonbonded.a/nb_kernel202_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel203.o .libs/libgmx.lax/libnonbonded.a/nb_kernel203_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel204.o .libs/libgmx.lax/libnonbonded.a/nb_kernel204_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel210.o .libs/libgmx.lax/libnonbonded.a/nb_kernel210_x86_64_sse.o .libs/libgmx.lax/libnonbonded.a/nb_kernel211.o .libs/libgmx.lax/libnonbonded.a/nb_kernel211_x86_64_sse.o .libs/libgmx.lax
[gmx-users] tests for gmx 4.5
Is there a proper set of tests for gmx 4.5 because neither ftp://ftp.gromacs.org/pub/tests/gmxtest-4.0.4.tgz or git clone git:// git.gromacs.org/regressiontests.git is working due to the several modifications done in gmx 4.5 including automatic thread for mdrun (I am using a Mac with dual core) and more warnings. Thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] gmx 4.5 issue with grompp
I am trying this test of mine: wget -c http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdbcompression=NOstructureId=1BVG; -O 1BVG.pdb grep 'ATOM ' 1BVG.pdb| Protein.pdb pdb2gmx -ff amber99sb -f Protein.pdb -o Protein2.pdb -p Protein.top -water spce -ignh editconf -bt triclinic -f Protein2.pdb -o Protein3.pdb -d 1.0 genbox -cp Protein3.pdb -o Protein_b4ion.pdb -p Protein.top -cs cat EOF | em.mdp define = -DFLEXIBLE integrator = cg ; steep nsteps = 200 constraints = none emtol= 1000.0 nstcgsteep = 10 ; do a steep every 10 steps of cg emstep = 0.01 ; used with steep nstcomm = 1 coulombtype = PME ns_type = grid rlist= 1.0 rcoulomb = 1.0 rvdw = 1.4 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 0 ; write coords every # step optimize_fft = yes EOF cat EOF | md.mdp integrator = md nsteps = 1000 dt = 0.002 constraints = all-bonds nstcomm = 1 ns_type = grid rlist= 1.2 rcoulomb = 1.1 rvdw = 1.0 vdwtype = shift rvdw-switch = 0.9 coulombtype = PME-Switch Tcoupl = v-rescale tau_t= 0.1 0.1 tc-grps = protein non-protein ref_t= 300 300 Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p= 0.5 compressibility = 4.5e-5 ref_p= 1.0 gen_vel = yes nstxout = 2 ; write coords every # step lincs-iter = 2 DispCorr = EnerPres optimize_fft = yes EOF grompp -f em.mdp -c Protein_b4ion.pdb -p Protein.top -o Protein_b4ion.tpr \cp Protein.top Protein_ion.top echo 13 | genion -s Protein_b4ion.tpr -o Protein_b4em.pdb -neutral -conc 0.15 -p Protein_ion.top -norandom \mv Protein_ion.top Protein.top grompp -f em.mdp -c Protein_b4em.pdb -p Protein.top -o em.tpr mdrun -v -deffnm em grompp -f md.mdp -c em.gro -p Protein.top -o md.tpr And it fails for the command above with: --- Program grompp, VERSION 4.5-beta1 Source code file: inputrec.c, line: 161 Software inconsistency error: Unknown epc value Any ideas? Thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: gromacs energies very different from other MD engine for the very same system and condition
First of all, thanks a lot guys, in special Ilja and Chris. Indeed, Ilja's observation proved to be corrected, and as Chris suggested, using the pdb instead of the gro for grompp and the energies matched. However, I am still uneasy with the fact that pdb2gmx_d and mdrun_d is not generating a gro with at least 6 decimals instead of the usual 3. Many thanks, Alan On Tue, Jul 27, 2010 at 20:34, gmx-users-requ...@gromacs.org wrote: Alan: you should try Ilja's suggestion, it was a good one. The idea is that during pdb2gmx you may have obtained a .gro file that was rounded and then you may have used this .gro as input to grompp and so your run did not start with the exact same coordinates in gromacs and namd. A similar test would be to be sure that you run grompp with the same .pdb file that you used in namd, etc. (or perhaps you already did that?) Actually, from what you post below I think that you have your answer. Use the orig .pdb into grompp and things should be ok, probably even in single precision, although the output .gro will be rounded as you see. PS: let's keep a positive mood. Chris. -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] gromacs energies very different from other MD engines for the very same system and conditions
Hi there, I have a very simple case of a tri alanine (AAA). You can use tleap from ambertools to create such peptide and save the pdb and amber's parameters. Then I do a single point calculation to get the potential energy. I am using mdin (amber input file) like: cat EOF | mdin Single point cntrl imin=0, maxcyc=0, ntmin=2, ntb=0, igb=0, cut=999, / EOF Then I test the same input parameters with Namd2, using namd.conf (Amber is not freely available, but AmberTools and Namd are): cat EOF | AAAamb_namd.conf outputEnergies 1 # Energy output frequency DCDfreq1 # Trajectory file frequency timestep 2 # in unit of fs temperature300 # Initial temp for velocity assignment cutoff 999 switching off # Turn off the switching functions PMEoff # Use PME for electrostatic calculation amber on # Specify this is AMBER force field parmfile AAAamb.prmtop # Input PARM file ambercoor AAAamb.inpcrd # Input coordinate file outputname AAAamb # Prefix of output files excludescaled1-4 1-4scaling 0.83 # =1/1.2, default is 1.0 minimize 0 EOF I have only a 0.001 kcal/mol absolute diff (or relative 0.0037%) for the Elec term, everything else is absolutely the same. Then comes gromacs. I convert my prmtop and inpcrd to gromacs top and gro with either acpype or amb2gmx and then doing a single point with file: cat EOF | SPE.mdp integrator = md nsteps = 0 dt = 0.001 constraints = none emtol= 10.0 emstep = 0.01 nstcomm = 1 ns_type = simple nstlist = 0 rlist= 0 rcoulomb = 0 rvdw = 0 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 1 pbc = no nstlog = 1 nstenergy = 1 nstvout = 1 nstfout = 1 nstxtcout = 1 comm_mode = ANGULAR EOF I got something like: Energies (kJ/mol) Bond Angle Ryckaert-Bell. LJ-14 Coulomb-14 1.77662e+023.19281e+014.55707e+012.48926e+019.40060e+02 LJ (SR) Coulomb (SR) PotentialKinetic En. Total Energy -9.21735e+00 -1.05005e+031.60848e+028.84934e+001.69697e+02 Temperature Pressure (bar) 2.28887e+010.0e+00 First question, why I have temperature and kinetic energy? Remember, it's a single point energy calculation, without any sort of coupling, 0 velocities and and gen_vel = no. Secondly, converting gromacs energies (kJ/mol) by dividing the terms by 4.184 and they don't match amber/namd results. See relative diffs (abs(g-a)/max(abs(a),abs(g))): Bond:5.87% Angle: 3.49% Dihe:0.14% vdW: 0.52% Elec:0.17% Pot.Tot: 5.90% I am very surprised to find this difference, in special for Bond since it's for this term essentially the same equation and parameters. Any ideas of what could be missing here? Many thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: gromacs energies very different from other MD engine for the very same system and condition
Thanks Ilja, On Tue, Jul 27, 2010 at 16:36, gmx-users-requ...@gromacs.org wrote: I think the bond terms differ simply due to the round off error. The gro file is worse than pdb when it comes to round off in Cartesian coordinates. You can confirm this is the case by taking your gro file and converting it back to pdb using gromacs tools and then use the resulting pdb (with the same round of as the gro file now) file from gromacs in NAMD. You should see the same numbers for bonded terms then. I doubt that would do any difference. Anyway, I tested with double precision and found out that my gro file is still rounded off like in single precision, i.e., my gro in double is the same in single and I was not expecting that. Example: pdb: 13 N ALA A 2 1.927 1.789 1.165 1.00 0.00 gro (single or double): 2ALA N 13 0.193 0.179 0.117 I was expecting gro when using pdb2gmx_d to be like: gro (single or double): 2ALA N 13 0.192700 0.178900 0.165000 Hummm I don't like this. Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] energies in amber, namd and gromacs
Hi there, I have a very simple case of a tri alanine (AAA). You can use tleap to create such peptide and save the pdb and amber's parameters. Then I do a single point calculation to get the potential energy. I am using mdin like: cat EOF | mdin Single point cntrl imin=0, maxcyc=0, ntmin=2, ntb=0, igb=0, cut=999, / EOF Then I test the same input parameters with Namd2, using namd.conf: cat EOF | AAAamb_namd.conf outputEnergies 1 # Energy output frequency DCDfreq1 # Trajectory file frequency timestep 2 # in unit of fs temperature300 # Initial temp for velocity assignment cutoff 999 switching off # Turn off the switching functions PMEoff # Use PME for electrostatic calculation amber on # Specify this is AMBER force field parmfile AAAamb.prmtop # Input PARM file ambercoor AAAamb.inpcrd # Input coordinate file outputname AAAamb # Prefix of output files excludescaled1-4 1-4scaling 0.83 # =1/1.2, default is 1.0 minimize 0 EOF I have only a 0.001 kcal/mol absolute diff (or relative 0.0037%) for the Elec term, everything else is absolutely the same. Then comes gromacs. I convert my prmtop and inpcrd to gromcs top and gro with either acpype or amb2gmx and then doing a single point with file: cat EOF | SPE.mdp integrator = md nsteps = 0 dt = 0.001 constraints = none emtol= 10.0 emstep = 0.01 nstcomm = 1 ns_type = simple nstlist = 0 rlist= 0 rcoulomb = 0 rvdw = 0 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 1 pbc = no nstlog = 1 nstenergy = 1 nstvout = 1 nstfout = 1 nstxtcout = 1 comm_mode = ANGULAR EOF Converting gromacs energies (kJ/mol) by dividing the terms by 4.184 and they don't match amber/namd results. See relative diffs (abs(g-a)/max(abs(a),abs(g))): Bond:5.87% Angle: 3.49% Dihe:0.14% vdW: 0.52% Elec:0.17% Pot.Tot: 5.90% I am very surprised to find this difference, in special for Bond since it's for this term essentially the same equation and parameters. Any ideas of what could be missing here? Many thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Help needed with ACPYPI
Hi there, I didn't have time to improve opls generation in ACPYPE. I need to put a Wiki about it for the moment, but to get the Opls atomtypes, use MKTOP: http://labmm.iq.ufrj.br/mktop/ Good luck, Alan On Tue, Jul 20, 2010 at 14:42, gmx-users-requ...@gromacs.org wrote: Hello all I want to study protein-ligand using OPLS ff of Gromacs. For Ligand topology preparation, I am using ACPYPI where I am getting 9 opls_x 1 1 C9__9 0.056600 0.0 ; qtot -0.253 in .itp file of ligand. And thus, atomtype opls_x is not recognised which leads to falal error This C9 is of the form R1=C9H-R2 for which I also searched the ffoplsaa.atp, but did not get any luck. Hope I made myself clear.. Any help will be highly appreciated. -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: amber parameters in gromacs
Hold on, you said *amber*, nevertheless you top has definitions for GROMOS**. Either you are mixing force fields here (which *bad*) or worse, your not using Amber FF, which is *really bad*. I would be helpful if you give the commands you're using for pdb2gmx and grompp. Besides, are you aware of ffamber and acpype? Since you said you have the parameters for glycerol you may not need to build the topology anew, but I do recommend looking at acpype.googlecode.com to know more about simulations involving amber ff and gromacs, besides links to important resources like ffamber. Cheers, Alan On Thu, Jul 1, 2010 at 09:13, gmx-users-requ...@gromacs.org wrote: Dear gromacs-users, I've been simulating a box of liquid glycerol. The parameter's I have used were taken from an article, whose authors achieved good agreement between their simulation and experiments. These authors used an amber force field and the software ORAC. I used exactly the same parameters as them for my topology and very similar settings in my mdp file. However I did not get the same results as them. Do you know why I get these different results? I am in doubt weather the top of my topology is correct, so I pasted it here: #define _FF_GROMOS96 #define _FF_GROMOS53A6 [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 12 yes 0.5 0.8333 [ atomtypes ] ;name at.num mass charge ptype sigma epsilon OA 8 0.000 0.000 A 0.34420.879228 C 6 0.000 0.000 A 0.38160.45803592 H 1 0.000 0.000 A 0 0 HC 1 0.000 0.000 A 0.27740.06573276 [ moleculetype ] Glycerol 3 [ atoms ] ; nr type resnr resid atom cgnr charge 1 OA 1 GLCR OAA1 -0.58515.9994 2 H 1 GLCR HAA1 0.3961.008 3 C 1 GLCR CAD1 0.18212.011 . I think, that by specifying comb-rule = 2 giving sigma and epsilon is correct instead of c6 and c12. The 0.5 for fudgeLJ and the 0.8333 for fudgeQQ are supposed to lower the 1-4 interaction. Regards, Rolf -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: amber parameters in gromacs
Hi Rolf, On Thu, Jul 1, 2010 at 10:23, gmx-users-requ...@gromacs.org wrote: I used the GROMOS FF but changed the parameters (sigma, epsilon, charges, 1-4 interaction, combination rule for LJ, bond length strength, dihedrals, angles) so that they are equal to the parameters used by the other authors with their AMBER FF. The equations uses to calculate the energy are the same, that is why I expected to get the same results. ...so I guess this assumption is not true. Why is it not possible to use these parameters? I understand that you're trying to simulate *only* glycerol and nothing else. In principle your idea does hold water, but in the end it's full of holes. GROMOS FF is conceived as an united-atom ff even if you have all protons explicit. The biggest difference among others I see is the way how dihedrals will be calculated. BTW, where's the reference to the article you mentioned? Do you want to rule out these potentials problems? Re-read the first email I sent and do check the links I provided. From there you can start to know how to use ffamber or, if you have your parameters in amber format (do you know how to use tleap from AmberTools to generate a prmtop and inpcrd files?), to use acpype (or amb2gmx) to convert them to gromacs format straightaway. Is there a way to get a topology of glycerol working with gromacs instead of writing it oneself? I've already tried the Prodrg Server but I didn't get proper results with this topology, either. The basic answer is yes and my attempt to to answer that is above. Cheers, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: question about [ pairs ] and interaction 1-4
Thanks Mark, here is the answer I got from Amber list and explains what I saw. Cheers, Alan This is an issue with the force field and has been noted several times before. I would take a look at the mailing list archive ( http://archive.ambermd.org) - search for phosphate hydrogen and you will see lots of relevant answers. For example: http://archive.ambermd.org/200408/0178.html The issue is that there is no VDW radii on OH hydrogens. One possible fix for this is to add a small VDW radii to the H atom. I would also suggest using shake (even during the minimization) which will help since it will keep the O-H bond length fixed. Essentially none of the force fields were ever really designed to be used without shake so you can get weird things happen if you are not using shake. Phosphate groups are an extreme case however. Essentially, with water and hydroxyl hydrogens it is assumed the H atom is effectively within the VDW sphere of the oxygen atom, hence why it has zero VDW radii. Phosphates have a huge electrostatic interaction which can effectively override this. Note though that having shake stops the H bond increasing in length so it effectively remains within the oxygen VDW sphere. This may be enough to prevent the catastrophe you are seeing. Alternatively consider creating a new atom type for hydroxyl group bonded to oxygen bonded to phosphorus adding the small VDW radii for the H atom. Note gaff has a hp atom type: hp 0.6000 0.0157 same to hs (be careful !) Which is listed as H bonded to phosphate. Note this is different from hydroxyl: ho 0. 0. OPLS Jorgensen, JACS,110,(1988),1657 in that it has a VDW radii. Good luck, All the best Ross -Original Message- From: Alan [mailto:alanwil...@gmail.com] Sent: Tuesday, June 15, 2010 4:17 AM To: AMBER Mailing List Subject: [AMBER] to understand 1-4 interactions in Amber FF Hi there, I have this molecule ATP, deprotonated, with 46 atoms and -1 net charge which topology was generated via Antechamber. I tested with sander, namd and gromacs (converting it via ACPYPE). The latter is not discussed here although the general result is similar to the former 2. Essentially I am doing a energy minimisation (EM) following these instructions (set only to emphasise the issue, not really for production): #AMBER 11 cat EOF | mdin Minimization cntrl imin=1, maxcyc=2000, ntmin=2, ntb=0, igb=0, cut=999, / sander -O -i mdin -o mdout -p HATP_AC.prmtop -c HATP_AC.inpcrd ambpdb -p HATP_AC.prmtop restrt HATP_amber.pdb mdout OUTPUT: NSTEP ENERGY RMSGMAX NAME NUMBER 1950 -2.2514E+08 5.9075E+13 3.4193E+14 O01 4 BOND= 35.0839 ANGLE = 124.4508 DIHED = 28.9012 VDWAALS = -8.5795 EEL = 933.8418 HBOND = 0. 1-4 VDW = 15.4554 1-4 EEL = * RESTRAINT = 0. NSTEP ENERGY RMSGMAX NAME NUMBER 2000 -1.3381E+07 2.0866E+11 1.2077E+12 HHO 1 BOND= 35.0845 ANGLE = 124.4511 DIHED = 28.9012 VDWAALS = -8.5795 EEL = 933.8418 HBOND = 0. 1-4 VDW = 15.4554 1-4 EEL = * RESTRAINT = 0. # NAMD 2.7b2 cat EOF | HATP_namd.conf outputEnergies 50 # Energy output frequency DCDfreq2 # Trajectory file frequency timestep 2 # in unit of fs temperature300 # Initial temp for velocity assignment cutoff 999 switching off # Turn off the switching functions PMEoff # Use PME for electrostatic calculation amber on # Specify this is AMBER force field parmfile HATP_AC.prmtop # Input PARM file ambercoor HATP_AC.inpcrd # Input coordinate file outputname HATP_namd # Prefix of output files excludescaled1-4 1-4scaling 0.83 # =1/1.2, default is 1.0 minimize 2000 EOF namd2 +p2 HATP_namd.conf | namd.log LINE MINIMIZER BRACKET: DX 1.29731e-05 1.06277e-05 DU -1.70323e-05 1.14306e-05 DUDX -2.62589 5.05233e-05 2.15101 LINE MINIMIZER REDUCING GRADIENT FROM 44.7384 TO 0.0447384 TIMING: 2000 CPU: 0.76958, 0.000377574/step Wall: 0.423322, 0.00021419/step, 0 hours remaining, 98.023438 MB of memory in use. ETITLE: TS BOND ANGLE DIHED IMPRP ELECTVDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG ENERGY:200031.2774 272.217233.5413 0. -2823.331323.6328 0. 0. 0. -2462.6627 0. -2462.6627 -2462.6627 0. vmd -parm7 HATP_AC.prmtop -rst7 HATP_AC.inpcrd HATP_namd.dcd I tried but I wish I could set the parameters in namd and sander so the energy results could
[gmx-users] Re: Adding Partial Charges for Small Molecules
Dear Nancy, Just completing what Justin did, see below. On Mon, Jun 14, 2010 at 03:10, gmx-users-requ...@gromacs.org wrote: Nancy wrote: Hi All, I am trying to add partial charges to nicotinamide adenine dinucleotide (NAD+), for input to molecular simulations. I have been using the UCSF Chimera program to do this. The total charge on this molecule should be -1 (assuming the ionization of NAD+ at pH ~7.0, see attached figure). When I add Gasteiger charges, the total charge sums up incorrectly to 0, even though the net charge specified in the drop-down box is -1. However, using the AM1-BCC method, the net charge correctly sums up to -1. The charge model used is Amber ff99SB. I have also noticed that the partial charges on individual atoms assigned when using the Sounds like a known issue with Chimera... http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-August/001732.html AM1-BCC method are generally of greater magnitude compared to charges assigned using the Gasteiger method. What is a good way to add correct partial charges to a small molecule? The best way is to follow the original methodology of the force field itself. The antechamber program of Amber is probably a good place to start to get Amber-compatible topologies. Also have a look here: http://www.pharmacy.manchester.ac.uk/bryce/amber#cof All of the above will require conversion to Gromacs-compatible formats, but there are scripts on the User Contribution site that might be suitable. Nancy, definitely, I wouldn't use Gasteiger here unless you're doing a comparison test. If you want something the closest to what AmberFF were done with the least hassle, look at http://q4md-forcefieldtools.org/REDS/ It simply worth the time reading and registering. Then, if I may suggest, you can try ACPYPE to generate your topology parameters in Gromacs format. ACPYPE indeed uses Antechamber, but as the link for the bug above, it may have the same issue with Gasteiger. However, as I said, I would use am1bcc, which is straightforward with ACPYPE, and so far I've been happy with the results, even comparing with REDS. Best regards, Alan -Justin The mol2 structure code (with incorrect Gasteiger charges) is written below (and attached as NAD.mol2 with corresponding PNG structure image). Thanks in advance, Nancy -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] question about [ pairs ] and interaction 1-4
Hi there, I mostly use ffamber and sometimes I look in oplsaa to understand how things are implemented in gromacs (4.0.5) I have an example here, where 2 atoms, in a phosphate (see http://en.wikipedia.org/wiki/File:1-hydrogenphosphate-3D-balls.png) in 1-4 interaction that have opposite charges (0.473 x -0.787) and when doing a EM, the H will move towards and basically join one of the Oxygen of the phosphate (coulomb force clearly acting, but no LJ repulsion?). The definitions in the top file are: [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 [ pairs ] ; ai ajfunct 1 4 1 ;HHO - O01 What I was expecting is since I declared the pair 1, 4 in [ pairs ] and the parameters to be set 0 by omission (or am wrong here?) that such interaction between atoms HHO and O01 shouldn't happen, but clearly it's not what I see. Yet I checked the manual, page 112 in particular. It is the first time I come across an example where I have 2 atom in 1-4 interaction with such a large opposite charges. Is the behaviour I see OK, although apparently rare? Many thanks in advance, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: acetonitrile from amber to gromacs
Dear Vedat, Thank you very much indeed. Things only get better with constructive feedbacks, either positive or negative. Glad you're managing well your problem. However, as I see, your problem now is in the tleap level. So, are you in amber mailing list? If so I would suggest to post your question there. If not, let me know and I try to post the question there (you may want to consider joining it, very useful, even for those who uses only ambertools). However, at first, I would go ahead and neglect the error. In the end, if you not happy, you can always adjust this particular parameter (in the itp file), since in principle a triple bond would mean a stronger bond, so implying in higher K-string constant. For how much to adjust? Well, you cannot even ever say that you got is correct; all you can get is a better or worse model and in the end it's up to you to set that. Nevertheless, be sure that you have the right protonation state and try to re-run your case putting CONECT info in the pdb just to check it. I hope it helps. Best, Alan On Fri, Jun 4, 2010 at 11:00, gmx-users-requ...@gromacs.org wrote: hi alan and all others, i love it. i've probably never seen such a helpful and constuctive answer to a question asked over the gmx user mailing list. following your instructions was very informative on the one hand and provided the results that i needed on the other. slightly modifying the the ch3cn.frcmod and -.prep files from the manchester site in accordance with a newer solvent model for acetonitrile of the year 2007 and feeding tleap with that data resulted in a ch3cn.lib file and afterwards in ch3cn.prmtop and ch3cn.inpcrd which i could use as input for acpype in order to generate .gro and .itp files. perfect. almost perfect, because in tleap i was not able to add the YC-YN triple bond (with the bond ... command) without generating an error message when saving my parameter files (saveAmberParm ... command). see the following output: bond C3N.1.C2 C3N.1.N1 T saveAmberParm C3N ch3cn.prmtop ch3cn.inpcrd Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. !FATAL ERROR !FATAL:In file [unitio.c], line 1778 !FATAL:Message: 1-4: cannot add bond 1 2 This may be caused by duplicate bond specifications; for example, explicit bond commands in addition to PDB conect records. ! !ABORTING. where could the second bond specification be, that avoids the specification of a triple bond T? there's no bonding information in the pdb file. a step earlier in tleap, i had to addAtomTypes YN and YC, however, there was no way to specify them with sp hybridization, but sp2 resulting in two lines each containing a single bond between these two atoms within the !entry.C3N.unit.connectivity table section of the ch3cn.lib file (seems to be a double bond). is this issue negligible, since the force constants and equilibrium angles (180 degrees) are already describing the right molecule? vedat Alan schrieb: Nice, glad you did progress. See below. On Thu, May 20, 2010 at 12:38, gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org wrote: thanks for your helpful hints. i updated acpype, created a pdb file with a single molecule and ran acpype -i ch3cn_210_single.pdb which generated an .itp and other interesting files. that's nice. (remember, i want to use gromacs with amber99sb force field and i downloaded 3 files from the amber site: ch3cn_210.pdb, frcmod.ch3cn,prep.ch3cn.have you ever seen their content?) 1) the charges do not match the ones listed in the prep.ch3cn file. shall i just change them by hand accordingly? It doesn't match because it's using am1bcc, which was parametrised to reproduce the RESP charges, but obviously (sqm is semi-empirical method, not like gaussian) it won't be accurate. However, you're right, if you have the RESP charges in prep.ch3cn just copy them by hand accordingly. Or even better, if you want to learn more about the whole stuff, double check if the parameters you got from the Manchester site are OK, why not trying q4md-forcefieldtools.org/RED/ http://q4md-forcefieldtools.org/RED/? Once you got the charges (they should be very close if not the same from prep.ch3cn), you can use acpype just to generate the topology by providing a c3n.MOL2 file with the charges calculated by RED and then using acpype -di c3n.mol2 -c user. 2) dummy atoms as listed in the prep.ch3cn are not present in the new .itp file. I guess you don't know how a prep file works, so see http://ambermd.org/doc/prep.html. 3) the force constants seem totally different. shall i again just adjust them to the original file obtained from the amber site? If using
[gmx-users] Re: acetonitrile from amber to gromacs
Nice, glad you did progress. See below. On Thu, May 20, 2010 at 12:38, gmx-users-requ...@gromacs.org wrote: thanks for your helpful hints. i updated acpype, created a pdb file with a single molecule and ran acpype -i ch3cn_210_single.pdb which generated an .itp and other interesting files. that's nice. (remember, i want to use gromacs with amber99sb force field and i downloaded 3 files from the amber site: ch3cn_210.pdb, frcmod.ch3cn,prep.ch3cn.have you ever seen their content?) 1) the charges do not match the ones listed in the prep.ch3cn file. shall i just change them by hand accordingly? It doesn't match because it's using am1bcc, which was parametrised to reproduce the RESP charges, but obviously (sqm is semi-empirical method, not like gaussian) it won't be accurate. However, you're right, if you have the RESP charges in prep.ch3cn just copy them by hand accordingly. Or even better, if you want to learn more about the whole stuff, double check if the parameters you got from the Manchester site are OK, why not trying q4md-forcefieldtools.org/RED/? Once you got the charges (they should be very close if not the same from prep.ch3cn), you can use acpype just to generate the topology by providing a c3n.MOL2 file with the charges calculated by RED and then using acpype -di c3n.mol2 -c user. 2) dummy atoms as listed in the prep.ch3cn are not present in the new .itp file. I guess you don't know how a prep file works, so see http://ambermd.org/doc/prep.html. 3) the force constants seem totally different. shall i again just adjust them to the original file obtained from the amber site? If using acpype with default mode, so you'd get GAFF parameters. You may want to try: acpype -di c3n.mol2 -c user -a amber However, it still may diff. If you read Jaime's paper and you agree with what he did, so you can copypaste his parameters as well. is there another way of using acpype, with a proper args list, that i should use in this situation? Read the Wikis in the acpype site and 'acpype -h'. I am always keen for suggestions. Another possible way, would be using tleap from AmberTools, generate just one molecule, save parameters and use acpype to convert from amber to gromacs, something like acpype -p c3n.prmtop -x c3n.inpcrd If doing so, you'd get the exactly Jaime's topology but in gromacs format (gro and top file, not itp, so you may need to adjust things in the top file in order to create a itp, but should be a simple task). BTW, how did you get this message cannot find template for residue C3N in our library? i got that message *within* the following output when running: acpype -i ch3cn_210.pdb [...] Warning: cannot find template for residue C3N in our library. You will not be able to save prmtop for this molecule. Warning: cannot find template for residue C3N in our library. You will not be able to save prmtop for this molecule. [gtkleap]$ #check C3N [gtkleap]$ saveamberparm C3N ch3cn_210_AC.prmtop ch3cn_210_AC.inpcrd Error: dparm pchg does not exist! ++end_quote+ ERROR: Sleap failed == Removing temporary files... ACPYPE FAILED: [Errno 2] No such file or directory: 'ch3cn_210_AC.inpcrd' Total time of execution: 7s Ah, ok, I should've know this... It's a fall back routine to try to use 'sleap', but sleap is broken in AmberTools 1.3 and 1.4, unfortunately. Thanks for trying acpype. Cheers, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: OPLS-AA/L force field
Dear Oliver, On Thu, May 20, 2010 at 13:21, gmx-users-requ...@gromacs.org wrote: I'm using GLYCAM06, so it involves a bit more effort to generate a .top and .gro file than just using pdb2gmx but I thought I'd leave it out as I just wanted to explain the method I use to include it. Apologies for the confusion! If you are familiar to ambertools (tleap mainly), so you can create your molecule there, save the amber parameters and use acpype to convert from amber to gromacs format. Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: acetonitrile from amber to gromacs
Dear Vedat, On Wed, May 19, 2010 at 20:36, gmx-users-requ...@gromacs.org wrote: @rui acpypi -i ch3cn_210.pdb says: cannot find template for residue C3N in our library. and indeed, there's no residue C3N in my ffamber99sb.rtp file (and i don't know, how to use it in order to generate my topology or even an rtp file?!) Have a bit of patience and try to read a bit more about ACPYPE. 1) Read the info there, I am sure you'll find it useful; 2) You'll learn that you need to have just one molecule in a pdb and not the whole box if you want the topologi of C3N. 3) It took me 2s to get the topology with acpype but months to write the code, so if you'd take some few minutes to read and use an updated version (it's not acpypi anymore BTW)... BTW, how did you get this message cannot find template for residue C3N in our library? acpype.googlecode.com Regards, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: OPLS-AA/L force field
Hi You Zou, Complementing Justin's message, I would invite you to take a look at acpype.googlecode.com. It's my attempt to address problems like yours. There's also links to some options besides ACPYPE. Bear in mind that you should know what you're doing. I would suggest you to read the Wiki's there as well as several references also indicated there. ACPYPE is far from being perfect but it can be very helpful. I have my own methodology where it would require using RED Server for accurate partial charge calculations (ACPYPE may use SQM, which is semi-empirical, via Antechamber), then ACPYPE (which is mostly designed for Amber FF) and then MKTOP for getting the oplsaa atom types. Feel free to contact. Best regards, Alan On Tue, May 18, 2010 at 01:28, gmx-users-requ...@gromacs.org wrote: Message: 2 Date: Mon, 17 May 2010 12:58:09 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] OPLS-AA/L force field To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4bf175a1.9040...@vt.edu Content-Type: text/plain; charset=UTF-8; format=flowed you zou wrote: Dear Users, I have one question about Drug-Enzyme Complex,Similar to tutorial If I want to use GROMOS96 43a1, I can use Prodrg Beta version for drug but If I want to use OPLS-AA/L all-atom force field I can use Prodrg Beta version server too, or not? No. You can't use two different force fields in one simulation system. If I can't use this server, how can I make .gro file and .itp file for drug that remove from initial .pdb file? There are several programs in the User Contributions from the website, x2top (which is distributed with Gromacs), or you can build the topology by hand. No matter what you choose, you need a thorough understanding of the mechanics of your chosen force field, methods of validation, and of course Chapter 5 in the Gromacs manual. http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: about SHAKE, SETTLE, LINCS and double x single precision
Hi Ran! Good point, in Lippert et al. they didn't use (or is not clear) thermostats. And yes, I guess you're right. Thanks Alan On Fri, May 14, 2010 at 09:27, gmx-users-requ...@gromacs.org wrote: Hi Alan, I don't think using single precision is much of a problem when using thermostats, regardless of the constraint on the water. See also Berks' comments: http://oldwww.gromacs.org/pipermail/gmx-users/2010-March/049137.html http://oldwww.gromacs.org/pipermail/gmx-users/2010-March/049152.html Ran. -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] about SHAKE, SETTLE, LINCS and double x single precision
Hi there, From what I've read and known, here in the list as well, one of the main reasons why Gromacs run in single precision is because it has LINCS, besides SHAKE, which I believe requires double precision for accuracy. I am drawing such conclusion (that can be wrong) partially based on Lippert, R. A., Bowers, K. J., Dror, R. O., Eastwood, M. P., Gregersen, B. A., Klepeis, J. L., Kolossvary, I., and Shaw, D. E. A common, avoidable source of error in molecular dynamics integrators. Journal of Chemical Physics 126, 4 (Jan. 2007), 046101–1–046101–2 However, in this letter article they didn't test with LINCS. I would love to hear some comments from Gromacs developers. When I started in MD, developing our own MD software, all was done in double precision, then came Gromacs blowing up this paradigm. (I am aware that even in Gromacs, there are routines that really requires double precision, e.g. normal mode analysis). Essentially I would like to understand better this double x single approach in MD re accuracy. Thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: how many dihedral angles should be included for the naphthalene molecule if I use oplsaa
I second Justin here, for Amber FF (which share essentially the same topology but with different parameters with OPLS/AA), the impropers dihedrals seems to be enough as for TRP. Just a side note, using ACPYPE (which uses antechamber in the core) to generate topologies for molecules like TRP, 6 extra impr. dihedrals are added, but clearly not necessary. You may want to try ACPYPE as I believe antechamber does a really good job getting the topology (even if in excess of imp. dih as for TRP and probably for napthalene), and of course check the literature as suggested by Justin. Alan On Wed, Apr 28, 2010 at 06:13, gmx-users-requ...@gromacs.org wrote: Ming Han wrote: 1__2 6__ // 3\/ \\ |||4| \\___ /\___// 5 7 I want to know if 1-2-3-6 torsion should be included? And if both 2-3-4-7 and 6-3-4-5 should be included? Thanks. I would think that proper dihedrals would not even be used for such a molecule. The fused ring systems will utilize impropers to stay planar. For example, the TRP side chain specifies no proper dihedrals within the indole side chain; only impropers are used, but maybe someone with more OPLS derivation experience can comment. You can also look into the literature. A simple Google search for napthalene OPLS (without the quotes) turns up tons of simulation papers. -Justin -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: converting parmbsc0 dihedrals to RB function
Hi Guillem, Many thanks for your clarification. I was lazy to find out and remember why psc0 was not ported to GMX by ffAmber previously and it was exactly because what you've said. And because I was not confident enough, I didn't implement that for acpypi, which I believe does better than amb2gmx in general, so I would be glad if you could take a look at it and if you could let me know which modifications you did to amb2gmx. I am taking plunge in this problem again and I'll try to come out with a solution based in what you suggest. Cheers, Alan On Fri, Apr 9, 2010 at 00:53, gmx-users-requ...@gromacs.org wrote: Right, the only dihedral angles that do not allow an exact translation to RB because of the phase are the ones involving the new parametrization for nucleic acids. Namely, it corrects the alpha/gamma transitions to get the populations of states right, thus avoiding the loss of helicity on the long run. For proteins, there's no difference at all, so you can use ffamber. I've used the combined approach you mention without problems. The only thing is that I do not use pdb2gmx. Rather I use amber's tools (leap+libraries, all free in ambertools) to get a topology, and then I use a slightly modified version of amb2gmx.pl script to get a gromacs topology. I only convert the new parmbsc0 dihedrals to type 1 if the phase does not allow a direct conversion to RB form. Typically you have three entries for the same dihedral, this is no problem at the itp level, grompp captures them all. With this approach I reproduced a torsional scan of parmbsc0 from amber md tool using gromacs, so I feel confident about it. Another option is to use the ffamber parameters and change the itp file including the new ones. I should also mention that I had problems importing the new dihedrals using pdb2gmx. IIRC, pdb2gmx will only use one definition for dihedral if type 1 or 3 is used. There was a new dihedral type that could be used in the development versions, but... for a reason it did not work out for me, don't recall exactly why. It could well be that it would have worked with more patience from my side. Hope this helped, somehow. You were on the right direction anyway. best, Guillem -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: converting parmbsc0 dihedrals to RB function
Hi Guillem! Thanks! and sorry, you don't need to look the code, just use it when trying amb2gmx and case you noticed something suspect I would be glad to be informed. So no need to waste your time other than when *really* needing to use amb2gmx. Your solution is what I have in mind and what I am doing to test. Thanks again, Alan On Fri, Apr 9, 2010 at 11:00, gmx-users-requ...@gromacs.org wrote: Hi Alan, I have no experience with acpypi, so I can't tell which one does better, or why... rdparm not being needed, that would be a strong point. Unfortunately, I'm running a bit short of time at the moment, so I can't really spend a lot of time looking into unknown codes, hope you understand... Nevertheless, the modifications are straightforward : if the phase of the dihedral in question is different than 0 or 180, then you should print the 3 dihedrals as type 1 - and converting the units -, instead of combining them as RB. I did not do anything else to amb2gmx. best of luck, Guillem -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: converting parmbsc0 dihedrals to RB function
I strongly advice you to contact Eric Sorin from ffAMBER project as he's onto that and you maybe can add to his efforts. http://ffamber.cnsm.csulb.edu/ Alan On Wed, Apr 7, 2010 at 11:00, gmx-users-requ...@gromacs.org wrote: I am trying to port the new parmbsc0 forcefield ( http://mmb.pcb.ub.es/PARMBSC0/frcmod.parmbsc0) into gromacs for DNA simulations. While unit conversions are sufficient to convert many of the parameters from AMBER to GROMACS format, dihedral angle conversion does not seem to be straight forward - the dihedral parameters need to be converted to the Ryckaert-Bellemans parameters. I went through the GROMACS 4.0 manual, especially equations 4.61-4.65 to understand the procedure. The procedure involves comparing the fourier expansion of the IUPAC convention of dihedral potential (equation 4.65) with the Ryckaert-Bellemans (RB) functional of dihedral potential (equation 4.62) to get the Cn's of the RB function. However, I am not able to understand how to account for the phase angles. (Also to note, the parmbsc0 forcefield contains phase angles other than 0 and 180.) -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: converting parmbsc0 dihedrals to RB function
From ffamber (in e.g. .../gromacs/top/ffamber99sbbon.itp): - impropers treated as propers in GROMACS to use correct AMBER analytical function - propers treated as RBs in GROMACS to use combine multiple AMBER torsions per quartet I followed these instructions while building acpypi (acpypi.googlecode.com/ ). You can study my code and see how the conversion is done (I put the details inside acpypi.py). I didn't test acpypi with an amber prmtop/inpcrd input with parmbsc0 parameters, but it would be interesting to see what I would get. Bear in mind that if parmbsc0 were simple to port, then it would have been done since the first version of ffamber, but I know Eric Sorin is working on that now. Alan On Wed, Apr 7, 2010 at 22:00, gmx-users-requ...@gromacs.org wrote: Dear Users, I am trying to port the new parmbsc0 forcefield (http://mmb.pcb.ub.es/PARMBSC0/frcmod.parmbsc0) into gromacs for DNA simulations. While unit conversions are sufficient to convert many of the parameters from AMBER to GROMACS format, dihedral angle conversion does not seem to be straight forward - the dihedral parameters need to be converted to the Ryckaert-Bellemans parameters. Why? GROMACS can probably do the non-RB form - IIRC you can implement a sum of multiple instances of 4.61 with different n. I went through the GROMACS 4.0 manual, especially equations 4.61-4.65 to understand the procedure. The procedure involves comparing the fourier expansion of the IUPAC convention of dihedral potential (equation 4.65) with the Ryckaert-Bellemans (RB) functional of dihedral potential (equation 4.62) to get the Cn's of the RB function. However, I am not able to understand how to account for the phase angles. (Also to note, the parmbsc0 forcefield contains phase angles other than 0 and 180.) Elegant conversion formulae require those angles to be convenient... Mark -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] about water models
Hello there, I was rereading [1] van der Spoel, D., van Maaren, P., and Berendsen, H. A systematic study of water models for molecular simulation: Derivation of water models optimized for use with a reaction field. Journal of Chemical Physics 108, 24 (June 1998), 10220–10230. and was wondering if there's something newer. I mean, I am looking for water models comparisons, maybe using different force fields (my interest is amber ff, but if oplsaa would nice). In the end I would like to hear from users here if SPC/E is as it seems the ultimate water model for simulations or proteins and DNA without lipids. And if using membranes, what would be the water model recommended. Suggestion of references for reading are more than welcome. Thanks, Alan -- Alan Wilter Sousa da Silva, D.Sc. PDBe group, PiMS project http://www.pims-lims.org/ EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK +44 (0)1223 492 583 (office) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: including a custom itp file in topology
Hi Jack, Look, if I understand well, what you want is to be able to something like tleap does for amber, where you load all the libs you need, including the ones you created for your ligand(s), and then generate the MD input files at once needing just the complexed pdb or mol2 as input. For pdb2gmx to do the same, you would need to tweak the files /gromacs/top/ffamber99sb.rtp, hdb etc., which I once considered doing that for acpypi but then it would add much more complexity for no much gain. What I hope is for the new *pdb2gmx* (gmx 4.1 maybe? or only for gmx 5.0?) to feature, among other things, this capability as you requested. Cheers, Alan On Thu, Jan 28, 2010 at 17:13, Jack Shultz j...@drugdiscoveryathome.comwrote: Hi, I was trying to figure out if there is a short-cut for what I'm doing. I have complexes that I'm trying to prep using pdb2gmx. The ligand does not have a standard residue name. The way I know this can work is seperating out the ligand and protein into seperate files and preping the ligand using acpypi and the protein using pdb2gmx. Then incorporating them into a single pdb complex and including a reference to the ligand.itp (generated by acpypi) into a complex topology file. Is there any shortcut to doing this? any way to reference the ligand's itp file when running pdb2gmx? -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- Alan Wilter Sousa da Silva, D.Sc. PDBe group, PiMS project http://www.pims-lims.org/ EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK +44 (0)1223 492 583 (office) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: including a custom itp file in topology
Hi Berk, If pdb2gmx will do what you said below, then for me the feature is delivered. To be sure, what I would like to have (and I guess Jack too) is: - one has a pdb with protetin + ligands (one or more) - have the topologies itp files for the ligands already created - run pdb2gmx on complex.pdb and have pdb2gmx to *know* about the ligands and generated the respective top and gro files ready for EM and MD. It is that what I understood Jack wants and what you said you have added to the coming pdb2gmx (for gmx 4.1?). Many thanks, Alan On Fri, Jan 29, 2010 at 09:28, gmx-users-requ...@gromacs.org wrote: From: Berk Hess g...@hotmail.com Hi, I don't understand exactly what is the requested feature here. I am currently reorganizing the force field setup in Gromacs to more cleanly support AMBER and CHARMM and adding some extra functionality. I started a discussion on the gmx-developers list on this topic. On feature I have added is that rtp, hdb, etc files no longer have fixed names and you can have multiple of them. So you can just put, e.g., a file called ligand.itp in your force field or current dir and pdb2gmx will read it. Berk -- Alan Wilter Sousa da Silva, D.Sc. PDBe group, PiMS project http://www.pims-lims.org/ EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK +44 (0)1223 492 583 (office) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: including a custom itp file in topology
Dear Berk, I beg your pardon, but I have to assume that what you wrote below is not correct so, right? Should it be 'ligand.rtp' instead of 'ligand.itp'? Once I have my hands on this new pdb2gmx, I believe I can tweak acpypi to generate rtp files as well (but hdb and else probably not). Cheers, Alan On Fri, Jan 29, 2010 at 11:00, gmx-users-requ...@gromacs.org wrote: of them. So you can just put, e.g., a file called ligand.itp in your force field or current dir and pdb2gmx will read it. -- Alan Wilter Sousa da Silva, D.Sc. PDBe group, PiMS project http://www.pims-lims.org/ EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK +44 (0)1223 492 583 (office) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
