Re: [gmx-users] transmembrane protein simulation
Hi, Yes, g_membed is the right tool for you. Please read the paper Wolf et al, J Comp Chem, 31 (2010) 2169-2174. You will find a detailed description of the insertion method and a quick manual. It will save you a lot of headache. Regards, Christopher 2011/1/24 Mohana lakshmi mohanaa.bioi...@gmail.com Dear all I am trying to run simulation of transmembrane protein, i am looking for better ways to setup protein with lipid membrane. initially i used VMD to insert protein with lipid membrane but it did not come out well, i got errors while running position restraint. i read about g_membed tool in gromacs, is it helpful for setting up transmembrane proteins also? Is there any other better ways to insert protein perfectly into the membrane? Please help me to overcome this problem. Thanks and regards -- Mohanalakshmi N -- 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
[gmx-users] Gromos96 manual and user guid
Dear All I need GROMOS96 manual and user guid for my work. Can you send it for me? Thanks in advance for your help. -- 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] PRODRG server
Dear Dr.justin Actually by doing this we are using two different force fields in one simulation. I had done it before and the result was that I discussed before in gmx-users(LINCS Error,Exploding system,Bad contacts between atoms) Then,this approch seems to doesn't work about my system. Then I want to find charges and charge groups for gromos 43A1 and replace them for my drug(to edit PRODRG file manually) and work totally in gromos 43A1. Unfortunately I can't obtain these parameter. Please let me have if you have it. Can I use some Ab Initio software for determining partial charges of my drug? for example ABINIT or Gaussian! Thanks in advance On Sat, Jan 22, 2011 at 8:03 PM, Justin A. Lemkul jalem...@vt.edu wrote: mohsen ramezanpour wrote: Ok then,I can use PRODRG server to generate .top and .gro files for drug. since it's reported charges are not very accurate ,we can replace all charges completely with them in 53A6(if was present). But it means we are working in 53A6 force field. then,we must generate .top and .gro files for our protein with 53A6 too. and work completely with 53A6. Am i right? thanks in advance That sounds like a reasonable approach. Be sure to validate the drug topology. In my experience, this procedure is pretty good, but you always have to convince reviewers... -Justin On Sat, Jan 22, 2011 at 4:43 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: mohsen ramezanpour wrote: Dear Justin I read your articles about PRODRG server,they were very useful. But I have a question: are charges of functional groups and generally other atom groups the same in all force fields? Because you have modified charges of your molecules by Gromos96 53A6 while prodrg server is generating topology files in 43A1. I want to know can I replace charges from gromos 53A6 or other forcefields? thanks in advance Charges are not the same between force fields. We did our study with 43A1 since that is what PRODRG purports to produce. I would say that our recommendations carry to other Gromos force fields, as well, but don't take charges from 43A1 and apply them to 53A6. Be consistent within the force field. The atom types produced by PRODRG are largely shared between 43A1 and 53A6, so if you *completely* replace all charges with those from 53A6, you should have a topology that is compatible with 53A6. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
Re: [gmx-users] transmembrane protein simulation
Dear Christopher, Thanks for your valuable suggestion. I ll try it. Thanks and regards -- Mohanalakshmi N -- 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 -- Mohanalakshmi N -- 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] transmembrane protein simulation
Dear Itamar, Thank you so much. The website you sent is very useful. Thanks and regards -- Mohanalakshmi N -- 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] PRODRG server
On 24/01/2011 10:06 PM, mohsen ramezanpour wrote: Dear Dr.justin Actually by doing this we are using two different force fields in one simulation. I had done it before and the result was that I discussed before in gmx-users(LINCS Error,Exploding system,Bad contacts between atoms) Then,this approch seems to doesn't work about my system. Sounds like you've re-learned the lessons here: http://www.gromacs.org/Documentation/How-tos/Parameterization Then I want to find charges and charge groups for gromos 43A1 and replace them for my drug(to edit PRODRG file manually) and work totally in gromos 43A1. Unfortunately I can't obtain these parameter. Please let me have if you have it. Can I use some Ab Initio software for determining partial charges of my drug? for example ABINIT or Gaussian! You should choose a force field based on the likelihood of being able to successfully make your observations. You want one that has a record of useful performance on similar systems, for which you can develop reasonably reliable parameters readily, test them suitably, and run simulations smoothly. Don't presuppose the form of the solution. Mark Thanks in advance On Sat, Jan 22, 2011 at 8:03 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: mohsen ramezanpour wrote: Ok then,I can use PRODRG server to generate .top and .gro files for drug. since it's reported charges are not very accurate ,we can replace all charges completely with them in 53A6(if was present). But it means we are working in 53A6 force field. then,we must generate .top and .gro files for our protein with 53A6 too. and work completely with 53A6. Am i right? thanks in advance That sounds like a reasonable approach. Be sure to validate the drug topology. In my experience, this procedure is pretty good, but you always have to convince reviewers... -Justin On Sat, Jan 22, 2011 at 4:43 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: mohsen ramezanpour wrote: Dear Justin I read your articles about PRODRG server,they were very useful. But I have a question: are charges of functional groups and generally other atom groups the same in all force fields? Because you have modified charges of your molecules by Gromos96 53A6 while prodrg server is generating topology files in 43A1. I want to know can I replace charges from gromos 53A6 or other forcefields? thanks in advance Charges are not the same between force fields. We did our study with 43A1 since that is what PRODRG purports to produce. I would say that our recommendations carry to other Gromos force fields, as well, but don't take charges from 43A1 and apply them to 53A6. Be consistent within the force field. The atom types produced by PRODRG are largely shared between 43A1 and 53A6, so if you *completely* replace all charges with those from 53A6, you should have a topology that is compatible with 53A6. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/justin
Re: [gmx-users] adding of a new force field in gromacs 4.5.1
On 24/01/2011 6:16 PM, mina Madah wrote: Dear all I use charmm27 as a default for making my force field file , and now I need .n2t file while charmm27 don't have .n2t file . I use oplsaa as a default for .n2t file and g_x2top and could not read this file . That simply won't work. The atom-naming schemes are totally different. Without knowing your overall objective (including why you think charmm27 is a good template, and why you think you need to use g_x2top), it's hard to say anything more. Mark this is my .n2t file : HHP -0.181.00801C 0.150 HHE2-0.12 1.00801C 0.150 CCPT0.145 12.0113C 0.150 C 0.150 C 0.150 CCE20.145 12.0113H 0.108 H 0.108 C 0.150 NNAB-0.514.00673H 0.108 C 0.150 B 0.0 NNAB2 -0.514.0067 3B 0.0 C 0.140 B 0.0 NNB3-0.514.0067 3B 0.0 B 0.0 B 0.0 NNB20 14.0067 3B 0.0 B 0.0 H 0.108 BBAN-0.510.8110 3H 0.108 C 0.140 N 0.123 BBAN2 -0.510.8110 3N 0.123 C 0.132 N 0.123 BBN30 10.8110 3N 0.123 N 0.123 N 0.123 BBN20.5 10.8110 3B 0.0 B 0.0 H 0.108 HH1B0.061.0080 1B 0.0 HH2B0.061.0080 1B 0.0 HHCB0.061.008 1C 0.108 HHCN0.061.008 1C 0.108 HH1N0.301.00801N 0.095 HH2N0.301.00801N 0.095 CCAB-0.12 12.0113C 0.150 C 0.150 B 0.0 CCAN0.5 12.011 3C 0.133 N 0.132 C 0.150 CCNH0.5 12.011 3C 0.133 N 0.132 H 0.108 CCBH0.5 12.011 3C 0.133 B 0.0 H 0.108 is my manner true? any help will highly appreciated. -- 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: Secondary structure loss in implicit solvent simulations
Hi 1) I am using Amber03 forcefield. 2) In most cases Yes, but in others, implicit solvent simulations tend to crash almost immediately (after reporting segmentation fault). 3) It generally takes less than a couple of 100 ps for the loss of the secondary structure. A few times, I even received .gro files at the end with all values as nan. Earlier I thought it might be a problem with equilibration, but I have tried to run energy-minimization more than once followed by position-restrained runs as well (to equilibrate H-atoms). But the end result hasn't changed. Thanks Regards Kush --- Michael Shirts: A few questions: 1) What force field are you using? 2) do you get the same answers with and without GPU acceleration? 3) How long does it take for secondary structure to disappear? 100's of ps? 10's of ns? -- Kushagra Singhal Promovendus, Computational Chemistry van 't Hoff Institute of Molecular Sciences Science Park 904, room C2.119 1098 XH Amsterdam, The Netherlands +31 205256965 Universiteit van Amsterdam k.sing...@uva.nl -- 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: Secondary structure loss in implicit solvent simulations
K. Singhal wrote: Hi 1) I am using Amber03 forcefield. 2) In most cases Yes, but in others, implicit solvent simulations tend to crash almost immediately (after reporting segmentation fault). 3) It generally takes less than a couple of 100 ps for the loss of the secondary structure. A few times, I even received .gro files at the end with all values as nan. Points 2 and 3 indicate that whatever simulations you're trying to perform are simply unstable. If they don't crash immediately, they're giving meaningless output, right? Earlier I thought it might be a problem with equilibration, but I have tried to run energy-minimization more than once followed by position-restrained runs as well (to equilibrate H-atoms). But the end result hasn't changed. Do you get the same effects if you run a normal simulation on CPU and not GPU? That information would be critical for properly diagnosing what's going on. If it's not GPU-specific, in all likelihood whatever you're doing is incorrect somewhere along the way. -Justin Thanks Regards Kush --- *Michael Shirts:* A few questions: 1) What force field are you using? 2) do you get the same answers with and without GPU acceleration? 3) How long does it take for secondary structure to disappear? 100's of ps? 10's of ns? -- Kushagra Singhal Promovendus, Computational Chemistry van 't Hoff Institute of Molecular Sciences Science Park 904, room C2.119 1098 XH Amsterdam, The Netherlands +31 205256965 Universiteit van Amsterdam k.sing...@uva.nl mailto:k.sing...@uva.nl -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Gromos96 manual and user guid
mohsen ramezanpour wrote: Dear All I need GROMOS96 manual and user guid for my work. Can you send it for me? This information is (unfortunately) proprietary. You have to purchase the GROMOS software suite to obtain it. -Justin Thanks in advance for your help. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] PRODRG server
mohsen ramezanpour wrote: Dear Dr.justin Actually by doing this we are using two different force fields in one simulation. I had done it before and the result was that I discussed before in gmx-users(LINCS Error,Exploding system,Bad contacts between atoms) Then,this approch seems to doesn't work about my system. Then I want to find charges and charge groups for gromos 43A1 and replace them for my drug(to edit PRODRG file manually) and work totally in gromos 43A1. Please keep your story consistent. In the last message, you said you wanted to work completely within 53A6, so I advised you on how to do that, now you say that you're trying to work completely within 43A1. Unfortunately I can't obtain these parameter. You certainly do have these parameters. 43A1 is part of the Gromacs installation; in the .rtp file you'll find all of the functional groups that were derived in 43A1, as applied to amino acids and a few other groups. Please let me have if you have it. Can I use some Ab Initio software for determining partial charges of my drug? for example ABINIT or Gaussian! My paper that you said you read has discussion and recommendations on this point. But be very clear: none of the QM methods we tested were able to reproduce the charges that are assigned to known functional groups since the Gromos parameterization methodology calls for empirical refinement. Thus, manual modification and thorough validation are always necessary. -Justin Thanks in advance On Sat, Jan 22, 2011 at 8:03 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: mohsen ramezanpour wrote: Ok then,I can use PRODRG server to generate .top and .gro files for drug. since it's reported charges are not very accurate ,we can replace all charges completely with them in 53A6(if was present). But it means we are working in 53A6 force field. then,we must generate .top and .gro files for our protein with 53A6 too. and work completely with 53A6. Am i right? thanks in advance That sounds like a reasonable approach. Be sure to validate the drug topology. In my experience, this procedure is pretty good, but you always have to convince reviewers... -Justin On Sat, Jan 22, 2011 at 4:43 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: mohsen ramezanpour wrote: Dear Justin I read your articles about PRODRG server,they were very useful. But I have a question: are charges of functional groups and generally other atom groups the same in all force fields? Because you have modified charges of your molecules by Gromos96 53A6 while prodrg server is generating topology files in 43A1. I want to know can I replace charges from gromos 53A6 or other forcefields? thanks in advance Charges are not the same between force fields. We did our study with 43A1 since that is what PRODRG purports to produce. I would say that our recommendations carry to other Gromos force fields, as well, but don't take charges from 43A1 and apply them to 53A6. Be consistent within the force field. The atom types produced by PRODRG are largely shared between 43A1 and 53A6, so if you *completely* replace all charges with those from 53A6, you should have a topology that is compatible with 53A6. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --
[gmx-users] pdb2gmx error_ resall.c, line: 321
Dear GROMACS users, I have received the following error when trying to convert a pdb file (containing N-methylated L- Leucine residue) to gro format. I am using ffG53a6 forcefield. Opening library file /usr/local/gromacs/share/gromacs/top/FF.dat Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43a2 force field (improved alkane dihedrals) 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 6: [DEPRECATED] Gromacs force field (see manual) 7: [DEPRECATED] Gromacs force field with hydrogens for NMR 8: Encad all-atom force field, using scaled-down vacuum charges 9: Encad all-atom force field, using full solvent charges 4 Opening library file ffG53a6.rtp Opening library file aminoacids.dat Opening library file aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file vdwradii.dat Entries in vdwradii.dat: 28 Opening library file dgsolv.dat Entries in dgsolv.dat: 7 Opening library file electroneg.dat Entries in electroneg.dat: 71 Opening library file elements.dat Entries in elements.dat: 218 Reading 16L6_6S17_start.pdb... WARNING: all CONECT records are ignored Read '6S17 ', 39 atoms Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 6 residues with 39 atoms chain #res #atoms 1 ' ' 6 39 All occupancies are one Opening library file ffG53a6.atp Atomtype 1 Reading residue database... (ffG53a6) Opening library file ffG53a6.rtp Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing impropers on same bond as a proper *--- Program pdb2gmx, VERSION 4.0.5 Source code file: resall.c, line: 321 Fatal error: in .rtp file at line: --- * Could you please let me know what could be the problem..? yours sincerely, Uday. -- 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 error_ resall.c, line: 321
On 24/01/2011 11:53 PM, udaya kiran wrote: Dear GROMACS users, I have received the following error when trying to convert a pdb file (containing N-methylated L- Leucine residue) to gro format. I am using ffG53a6 forcefield. Opening library file /usr/local/gromacs/share/gromacs/top/FF.dat Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43a2 force field (improved alkane dihedrals) 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 6: [DEPRECATED] Gromacs force field (see manual) 7: [DEPRECATED] Gromacs force field with hydrogens for NMR 8: Encad all-atom force field, using scaled-down vacuum charges 9: Encad all-atom force field, using full solvent charges 4 Opening library file ffG53a6.rtp Opening library file aminoacids.dat Opening library file aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file vdwradii.dat Entries in vdwradii.dat: 28 Opening library file dgsolv.dat Entries in dgsolv.dat: 7 Opening library file electroneg.dat Entries in electroneg.dat: 71 Opening library file elements.dat Entries in elements.dat: 218 Reading 16L6_6S17_start.pdb... WARNING: all CONECT records are ignored Read '6S17 ', 39 atoms Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 6 residues with 39 atoms chain #res #atoms 1 ' ' 6 39 All occupancies are one Opening library file ffG53a6.atp Atomtype 1 Reading residue database... (ffG53a6) Opening library file ffG53a6.rtp Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing impropers on same bond as a proper *--- Program pdb2gmx, VERSION 4.0.5 Source code file: resall.c, line: 321 Fatal error: in .rtp file at line: --- * Could you please let me know what could be the problem..? You've broken the format of the .rtp file used in ffG53a6. Use the diff tool to compare the before and after versions. Be sure you are using unix-style line endings. 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
Re: [gmx-users] pdb2gmx error_ resall.c, line: 321
of the atom type Opening library file atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file vdwradii.dat Entries in vdwradii.dat: 28 Opening library file dgsolv.dat Entries in dgsolv.dat: 7 Opening library file electroneg.dat Entries in electroneg.dat: 71 Opening library file elements.dat Entries in elements.dat: 218 Reading 16L6_6S17_start.pdb... WARNING: all CONECT records are ignored Read '6S17 ', 39 atoms Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 6 residues with 39 atoms chain #res #atoms 1 ' ' 6 39 All occupancies are one Opening library file ffG53a6.atp Atomtype 1 Reading residue database... (ffG53a6) Opening library file ffG53a6.rtp Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing impropers on same bond as a proper *--- Program pdb2gmx, VERSION 4.0.5 Source code file: resall.c, line: 321 Fatal error: in .rtp file at line: --- * Could you please let me know what could be the problem..? yours sincerely, Uday. -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110124/de7bf383/attachment-0001.html -- Message: 4 Date: Tue, 25 Jan 2011 00:08:03 +1100 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] pdb2gmx error_ resall.c, line: 321 To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4d3d79b3.5040...@anu.edu.au Content-Type: text/plain; charset=iso-8859-1 On 24/01/2011 11:53 PM, udaya kiran wrote: Dear GROMACS users, I have received the following error when trying to convert a pdb file (containing N-methylated L- Leucine residue) to gro format. I am using ffG53a6 forcefield. Opening library file /usr/local/gromacs/share/gromacs/top/FF.dat Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43a2 force field (improved alkane dihedrals) 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 6: [DEPRECATED] Gromacs force field (see manual) 7: [DEPRECATED] Gromacs force field with hydrogens for NMR 8: Encad all-atom force field, using scaled-down vacuum charges 9: Encad all-atom force field, using full solvent charges 4 Opening library file ffG53a6.rtp Opening library file aminoacids.dat Opening library file aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file vdwradii.dat Entries in vdwradii.dat: 28 Opening library file dgsolv.dat Entries in dgsolv.dat: 7 Opening library file electroneg.dat Entries in electroneg.dat: 71 Opening library file elements.dat Entries in elements.dat: 218 Reading 16L6_6S17_start.pdb... WARNING: all CONECT records are ignored Read '6S17 ', 39 atoms Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 6 residues with 39 atoms chain #res #atoms 1 ' ' 6 39 All occupancies are one Opening library file ffG53a6.atp Atomtype 1 Reading residue database... (ffG53a6) Opening library file ffG53a6.rtp Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing impropers on same bond as a proper *--- Program pdb2gmx, VERSION 4.0.5 Source code file: resall.c, line: 321 Fatal error: in .rtp file at line: --- * Could you please let me know what could be the problem..? You've broken the format of the .rtp file used in ffG53a6. Use the diff tool to compare the before and after versions. Be sure you are using unix-style line endings. Mark -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments
Re: [gmx-users] Error in generating DPPC using grompp
shobana visolingam wrote: thanks. i read chapter 5 and i saw the DPPC topology in the membrane protein tutorial but i still cant find what's wrong with my topology format. below is how my topol.top file looks like #include ffgmx_lipid.itp [ moleculetype ] ; Namenrexcl Protein_A 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1CH3 1DPPC C1 1 0.124 15.035 ; snip ; Include DPPC chain topology #include DPPC.itp This doesn't make any sense. You've defined a Protein_A moleculetype containing DPPC, then you're including a chain topology for it (again) here. snip *and my ffgmxbon_lipid.itp file is:* [ bondtypes ] ; ij funcb0 kb CO1 0.12300 502080. C OM1 0.12500 418400. C OA1 0.13600 376560. CN1 0.13300 418400. C NT1 0.13300 376560. C NL1 0.13300 376560. CH1 OA1 0.14300 334720. CH1N1 0.14700 376560. CH1 NT1 0.14700 376560. CH1 NL1 0.14700 376560. CH1C1 0.15300 334720. CH1 CH11 0.15300 334720. CH2 OM1 0.14300 376560. CH2 OA1 0.14300 334720. ; get the constraint distances: #include ff_dum.itp [ constrainttypes ] ; now the constraints for the rigid NH3 groups MNH3C2 DC_MNC1 MNH3 CB2 DC_MNC1 MNH3 CHE2 DC_MNC1 MNH3 CH12 DC_MNC2 MNH3 CH22 DC_MNC2 MNH3 MNH32 DC_MNMN ; and the angle-constraints for OH and SH groups in proteins: CH2 HS2 DC_CS CH2 HO2 DC_CO CH1 HO2 DC_CO CB HO2 DC_CO CHO2 DC_CO PHO2 DC_PO [ angletypes ] ; ijk func th0 cth HO OAC1 109.500 397.480 HO OA CH11 109.500 397.480 HO OA CH21 109.500 397.480 HO OA CB1 109.500 397.480 HO OA CHE1 109.500 397.480 P OA HO1 109.500 397.480 CS1 OA HO1 109.500 397.480 CS2 OA HO1 109.500 397.480 HW OW HW1 109.500 502.080 CH1NC1 122.000 502.080 CH2NC1 122.000 502.080 CH2N CH11 116.000 502.080 CH3NC1 117.000 502.080 CH3N CH11 125.000 502.080 CH3N CH21 125.000 502.080 HNC1 123.000 292.880 .. .. [ dihedraltypes ] ; il funcq0 cq NR5* NR52 0.000 167.360 NR5* NR5*2 0.000 167.360 CO2 0.000 167.360 C OM2 0.000 167.360 C NT2 0.000 167.360 . . [ dihedraltypes ] ; jk func phi0 cp mult C OA1 180.000 16.736 2 CN1 180.000 33.472 2 C NT1 180.000 33.472 2 C NL1 0.000 3.766 3 CH1 OA1 0.000 1.255 3 CH1N1 180.000 0.418 6 CH1 NT1 0.000 3.766 6 CH1 NL1 0.000 3.766 3 CH1C1 0.000 0.418 6 CH1 CH11 0.000 5.858 3 CH2 OA1 0.000 1.255 3 CH2N1 180.000 0.418 6 CH2 NT1 0.000 3.766 6 CH2 NL1 0.000 3.766 3 CH2C1 0.000 0.418 6 CH2 CH11 0.000 5.858 3 CH2 CH21 0.000 5.858 3 CB OA1 180.000 7.113 2 CB NT1 180.000 33.472 2 CBC1 180.000 5.858 2 CB CH21 0.000 0.418 6 CB CR611 180.000 41.840 2 CHE OA1 180.000 7.113 2 CHE NT1 180.000 33.472 2 CHEC1 180.000 5.858 2 CHE CH21 0.000 0.418 6 CHE CR611 180.000 41.840 2 S CH21 0.000 2.929 3 SS1 0.000 16.736 2 FE NR51 0.000 0.000 4 NZC1 180.000 33.472 2 NEC1 180.000 33.472 2 NE CH21 180.000 0.418 6 ; two or three dihedral potentials are needed over some bonds, ; put the parameters in your topology manually ;P OA1 0.000 1.046 3 ;P OA1 0.000 3.138 2 OS CH21 0.000 3.766 3 ; OSP1 0.000 1.046 3 ; OS
[gmx-users] Atomtype HW not found when using grompp for energy minimization
Hello, I get the following error when I try to run grompp cpmmand for energy minimization in GROMACS of DPPC membrane ... checking input for internal consistency... processing topology... --- Program grompp, VERSION 4.0.7 Source code file: toppush.c, line: 843 Fatal error: Atomtype HW not found the topology file of the DPPC contains: -- ; This is your topology file ; 1SOL OW1 -2.449 -4.190 -1.80 ; ; Include chain topologies #include ffG53a6_lipid.itp #include dppc.itp ; Include water topology ;include spc.itp ; Include ion topologies ;include ions.itp ; System specifications [ system ] 128-Lipid DPPC Bilayer [ molecules ] ; molecule name nr. DPPC 128 SOL 3655 I am using ffG53a6 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
Re: [gmx-users] Atomtype HW not found when using grompp for energy minimization
Parul tew wrote: Hello, I get the following error when I try to run grompp cpmmand for energy minimization in GROMACS of DPPC membrane ... checking input for internal consistency... processing topology... --- Program grompp, VERSION 4.0.7 Source code file: toppush.c, line: 843 Fatal error: Atomtype HW not found Per the tutorial, step 2: Non-bonded interactions involving atom type HW are also present; since these are all zero you can delete these lines as well, or otherwise rename HW as H to be consistent with the GROMOS96 53a6 naming convention. the topology file of the DPPC contains: -- ; This is your topology file ; 1SOL OW1 -2.449 -4.190 -1.80 ; ; Include chain topologies #include ffG53a6_lipid.itp #include dppc.itp ; Include water topology ;include spc.itp ; Include ion topologies ;include ions.itp You're going to have problems here, as well. You've commented out the water and ion topologies. The next fatal error is surely going to be Moleculetype SOL not defined or the like. -Justin ; System specifications [ system ] 128-Lipid DPPC Bilayer [ molecules ] ; molecule name nr. DPPC 128 SOL 3655 I am using ffG53a6 thanks -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] using Berger Lipids in gromacs 4.5.3
Dear Justin, Thanks for pointing out :) much appreciated. I tried selecting 1 and the process seemed to stop after the work Atomtype 1, please see below: pdb2gmx -f prot_moved.pdb -o prot_pdb2gmx.pdb -p prot.top -ter -asp -his :-) G R O M A C S (-: GROningen MAchine for Chemical Simulation :-) VERSION 4.5.3 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) pdb2gmx (-: Option Filename Type Description -f prot_moved.pdb InputStructure file: gro g96 pdb tpr etc. -o prot_pdb2gmx.pdb Output Structure file: gro g96 pdb etc. -pprot.top Output Topology file -i posre.itp Output Include file for topology -n clean.ndx Output, Opt. Index file -q clean.pdb Output, Opt. Structure file: gro g96 pdb etc. Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint0 Set the nicelevel -chainsepenum id_or_ter Condition in PDB files when a new chain and molecule_type should be started: id_or_ter, id_and_ter, ter, id or interactive -ff string select Force field, interactive by default. Use -h for information. -water enum select Water model to use: select, none, spc, spce, tip3p, tip4p or tip5p -[no]inter bool no Set the next 8 options to interactive -[no]ss bool no Interactive SS bridge selection -[no]ter bool yes Interactive termini selection, iso charged -[no]lys bool no Interactive Lysine selection, iso charged -[no]arg bool no Interactive Arganine selection, iso charged -[no]asp bool yes Interactive Aspartic Acid selection, iso charged -[no]glu bool no Interactive Glutamic Acid selection, iso charged -[no]gln bool no Interactive Glutamine selection, iso neutral -[no]his bool yes Interactive Histidine selection, iso checking H-bonds -angle real 135 Minimum hydrogen-donor-acceptor angle for a H-bond (degrees) -distreal 0.3 Maximum donor-acceptor distance for a H-bond (nm) -[no]una bool no Select aromatic rings with united CH atoms on Phenylalanine, Tryptophane and Tyrosine -[no]ignhbool no Ignore hydrogen atoms that are in the pdb file -[no]missing bool no Continue when atoms are missing, dangerous -[no]v bool no Be slightly more verbose in messages -posrefc real 1000Force constant for position restraints -vsite enum noneConvert atoms to virtual sites: none, hydrogens or aromatics -[no]heavyh bool no Make hydrogen atoms heavy -[no]deuterate bool no Change the mass of hydrogens to 2 amu -[no]chargegrp bool yes Use charge groups in the rtp file -[no]cmapbool yes Use cmap torsions (if enabled in the rtp file) -[no]renum bool no Renumber the residues consecutively in the output -[no]rtpres bool no Use rtp entry names as residue names Select the Force Field: From current directory: 1: GROMOS96 53A6 force field, extended to include Berger lipid parameters From '/usr/remote/gromacs/4.5.3/share/gromacs/top': 2: AMBER03 force field (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003) 3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995) 4: AMBER96 force field (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996) 5: AMBER99 force field (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000) 6: AMBER99SB force field (Hornak et al., Proteins 65, 712-725, 2006) 7:
Re: [gmx-users] using Berger Lipids in gromacs 4.5.3
NG HUI WEN wrote: Dear Justin, Thanks for pointing out :) much appreciated. I tried selecting 1 and the process seemed to stop after the work Atomtype 1, please see below: pdb2gmx -f prot_moved.pdb -o prot_pdb2gmx.pdb -p prot.top -ter -asp -his :-) G R O M A C S (-: GROningen MAchine for Chemical Simulation :-) VERSION 4.5.3 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) pdb2gmx (-: Option Filename Type Description -f prot_moved.pdb InputStructure file: gro g96 pdb tpr etc. -o prot_pdb2gmx.pdb Output Structure file: gro g96 pdb etc. -pprot.top Output Topology file -i posre.itp Output Include file for topology -n clean.ndx Output, Opt. Index file -q clean.pdb Output, Opt. Structure file: gro g96 pdb etc. Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint0 Set the nicelevel -chainsepenum id_or_ter Condition in PDB files when a new chain and molecule_type should be started: id_or_ter, id_and_ter, ter, id or interactive -ff string select Force field, interactive by default. Use -h for information. -water enum select Water model to use: select, none, spc, spce, tip3p, tip4p or tip5p -[no]inter bool no Set the next 8 options to interactive -[no]ss bool no Interactive SS bridge selection -[no]ter bool yes Interactive termini selection, iso charged -[no]lys bool no Interactive Lysine selection, iso charged -[no]arg bool no Interactive Arganine selection, iso charged -[no]asp bool yes Interactive Aspartic Acid selection, iso charged -[no]glu bool no Interactive Glutamic Acid selection, iso charged -[no]gln bool no Interactive Glutamine selection, iso neutral -[no]his bool yes Interactive Histidine selection, iso checking H-bonds -angle real 135 Minimum hydrogen-donor-acceptor angle for a H-bond (degrees) -distreal 0.3 Maximum donor-acceptor distance for a H-bond (nm) -[no]una bool no Select aromatic rings with united CH atoms on Phenylalanine, Tryptophane and Tyrosine -[no]ignhbool no Ignore hydrogen atoms that are in the pdb file -[no]missing bool no Continue when atoms are missing, dangerous -[no]v bool no Be slightly more verbose in messages -posrefc real 1000Force constant for position restraints -vsite enum noneConvert atoms to virtual sites: none, hydrogens or aromatics -[no]heavyh bool no Make hydrogen atoms heavy -[no]deuterate bool no Change the mass of hydrogens to 2 amu -[no]chargegrp bool yes Use charge groups in the rtp file -[no]cmapbool yes Use cmap torsions (if enabled in the rtp file) -[no]renum bool no Renumber the residues consecutively in the output -[no]rtpres bool no Use rtp entry names as residue names Select the Force Field: From current directory: 1: GROMOS96 53A6 force field, extended to include Berger lipid parameters From '/usr/remote/gromacs/4.5.3/share/gromacs/top': 2: AMBER03 force field (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003) 3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995) 4: AMBER96 force field (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996) 5: AMBER99 force field (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000) 6: AMBER99SB force field (Hornak et al., Proteins 65,
RE: [gmx-users] using Berger Lipids in gromacs 4.5.3
Hi Justin, Thanks for your reply. I am using linux on a cluster remotely. It is made up of Hewlett Packard ProLiant DL160 compute nodes. I didn't see any ._ appearing in my gromos53a6_lipid.ff folder. Huiwen -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Monday, January 24, 2011 10:14 PM To: Gromacs Users' List Subject: Re: [gmx-users] using Berger Lipids in gromacs 4.5.3 NG HUI WEN wrote: Dear Justin, Thanks for pointing out :) much appreciated. I tried selecting 1 and the process seemed to stop after the work Atomtype 1, please see below: pdb2gmx -f prot_moved.pdb -o prot_pdb2gmx.pdb -p prot.top -ter -asp -his :-) G R O M A C S (-: GROningen MAchine for Chemical Simulation :-) VERSION 4.5.3 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) pdb2gmx (-: Option Filename Type Description -f prot_moved.pdb InputStructure file: gro g96 pdb tpr etc. -o prot_pdb2gmx.pdb Output Structure file: gro g96 pdb etc. -pprot.top Output Topology file -i posre.itp Output Include file for topology -n clean.ndx Output, Opt. Index file -q clean.pdb Output, Opt. Structure file: gro g96 pdb etc. Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint0 Set the nicelevel -chainsepenum id_or_ter Condition in PDB files when a new chain and molecule_type should be started: id_or_ter, id_and_ter, ter, id or interactive -ff string select Force field, interactive by default. Use -h for information. -water enum select Water model to use: select, none, spc, spce, tip3p, tip4p or tip5p -[no]inter bool no Set the next 8 options to interactive -[no]ss bool no Interactive SS bridge selection -[no]ter bool yes Interactive termini selection, iso charged -[no]lys bool no Interactive Lysine selection, iso charged -[no]arg bool no Interactive Arganine selection, iso charged -[no]asp bool yes Interactive Aspartic Acid selection, iso charged -[no]glu bool no Interactive Glutamic Acid selection, iso charged -[no]gln bool no Interactive Glutamine selection, iso neutral -[no]his bool yes Interactive Histidine selection, iso checking H-bonds -angle real 135 Minimum hydrogen-donor-acceptor angle for a H-bond (degrees) -distreal 0.3 Maximum donor-acceptor distance for a H-bond (nm) -[no]una bool no Select aromatic rings with united CH atoms on Phenylalanine, Tryptophane and Tyrosine -[no]ignhbool no Ignore hydrogen atoms that are in the pdb file -[no]missing bool no Continue when atoms are missing, dangerous -[no]v bool no Be slightly more verbose in messages -posrefc real 1000Force constant for position restraints -vsite enum noneConvert atoms to virtual sites: none, hydrogens or aromatics -[no]heavyh bool no Make hydrogen atoms heavy -[no]deuterate bool no Change the mass of hydrogens to 2 amu -[no]chargegrp bool yes Use charge groups in the rtp file -[no]cmapbool yes Use cmap torsions (if enabled in the rtp file) -[no]renum bool no Renumber the residues consecutively in the output -[no]rtpres bool no Use rtp entry
Re: [gmx-users] PRODRG server
mohsen ramezanpour wrote: Thanks for your guidance. I looked that file,But I think the name of functional groups are different in .rtp file because I can't find no one of them in this file. Functional group names are not in the .rtp files. You locate applicable functional groups by knowing the residues in which they occur. please let me know how can I know the correct name f or functional groups for example:HYDROXYL,CARBOXYL,HALO,AMINO and ... All of these except halogens exist in common amino acids. If you have many non-standard groups (i.e. those that don't typically occur in biomolecules), then perhaps your choice of force field was a poor one. As Mark said, don't presuppose the solution. -Justin Thanks in advance for your help On Mon, Jan 24, 2011 at 4:01 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: mohsen ramezanpour wrote: Dear Dr.justin Actually by doing this we are using two different force fields in one simulation. I had done it before and the result was that I discussed before in gmx-users(LINCS Error,Exploding system,Bad contacts between atoms) Then,this approch seems to doesn't work about my system. Then I want to find charges and charge groups for gromos 43A1 and replace them for my drug(to edit PRODRG file manually) and work totally in gromos 43A1. Please keep your story consistent. In the last message, you said you wanted to work completely within 53A6, so I advised you on how to do that, now you say that you're trying to work completely within 43A1. Unfortunately I can't obtain these parameter. You certainly do have these parameters. 43A1 is part of the Gromacs installation; in the .rtp file you'll find all of the functional groups that were derived in 43A1, as applied to amino acids and a few other groups. Please let me have if you have it. Can I use some Ab Initio software for determining partial charges of my drug? for example ABINIT or Gaussian! My paper that you said you read has discussion and recommendations on this point. But be very clear: none of the QM methods we tested were able to reproduce the charges that are assigned to known functional groups since the Gromos parameterization methodology calls for empirical refinement. Thus, manual modification and thorough validation are always necessary. -Justin Thanks in advance On Sat, Jan 22, 2011 at 8:03 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: mohsen ramezanpour wrote: Ok then,I can use PRODRG server to generate .top and .gro files for drug. since it's reported charges are not very accurate ,we can replace all charges completely with them in 53A6(if was present). But it means we are working in 53A6 force field. then,we must generate .top and .gro files for our protein with 53A6 too. and work completely with 53A6. Am i right? thanks in advance That sounds like a reasonable approach. Be sure to validate the drug topology. In my experience, this procedure is pretty good, but you always have to convince reviewers... -Justin On Sat, Jan 22, 2011 at 4:43 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: mohsen ramezanpour wrote: Dear Justin I read your articles about PRODRG server,they were very useful. But I have a question: are charges of functional groups and generally other atom groups the same in all force fields? Because you have modified charges of your molecules by Gromos96 53A6 while prodrg server is generating topology files in 43A1. I want to know can I replace charges from gromos 53A6 or other forcefields? thanks in advance Charges are not the same between force fields. We did our study with 43A1 since that is what PRODRG purports to produce. I would say that our recommendations carry to other Gromos force fields, as well, but don't take charges from 43A1
Re: [gmx-users] using Berger Lipids in gromacs 4.5.3
NG HUI WEN wrote: Hi Justin, Thanks for your reply. I am using linux on a cluster remotely. It is made up of Hewlett Packard ProLiant DL160 compute nodes. I didn't see any ._ appearing in my gromos53a6_lipid.ff folder. Can you send me a tarball of your gromos53a6_lipid.ff folder (off-list) so I can try to troubleshoot this? Your input .pdb file would be useful, as well. -Justin Huiwen -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Monday, January 24, 2011 10:14 PM To: Gromacs Users' List Subject: Re: [gmx-users] using Berger Lipids in gromacs 4.5.3 NG HUI WEN wrote: Dear Justin, Thanks for pointing out :) much appreciated. I tried selecting 1 and the process seemed to stop after the work Atomtype 1, please see below: pdb2gmx -f prot_moved.pdb -o prot_pdb2gmx.pdb -p prot.top -ter -asp -his :-) G R O M A C S (-: GROningen MAchine for Chemical Simulation :-) VERSION 4.5.3 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) pdb2gmx (-: Option Filename Type Description -f prot_moved.pdb InputStructure file: gro g96 pdb tpr etc. -o prot_pdb2gmx.pdb Output Structure file: gro g96 pdb etc. -p prot.top Output Topology file -i posre.itp Output Include file for topology -n clean.ndx Output, Opt. Index file -q clean.pdb Output, Opt. Structure file: gro g96 pdb etc. Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint0 Set the nicelevel -chainsep enum id_or_ter Condition in PDB files when a new chain and molecule_type should be started: id_or_ter, id_and_ter, ter, id or interactive -ff string select Force field, interactive by default. Use -h for information. -water enum select Water model to use: select, none, spc, spce, tip3p, tip4p or tip5p -[no]inter bool no Set the next 8 options to interactive -[no]ss bool no Interactive SS bridge selection -[no]ter bool yes Interactive termini selection, iso charged -[no]lys bool no Interactive Lysine selection, iso charged -[no]arg bool no Interactive Arganine selection, iso charged -[no]asp bool yes Interactive Aspartic Acid selection, iso charged -[no]glu bool no Interactive Glutamic Acid selection, iso charged -[no]gln bool no Interactive Glutamine selection, iso neutral -[no]his bool yes Interactive Histidine selection, iso checking H-bonds -angle real 135 Minimum hydrogen-donor-acceptor angle for a H-bond (degrees) -distreal 0.3 Maximum donor-acceptor distance for a H-bond (nm) -[no]una bool no Select aromatic rings with united CH atoms on Phenylalanine, Tryptophane and Tyrosine -[no]ignhbool no Ignore hydrogen atoms that are in the pdb file -[no]missing bool no Continue when atoms are missing, dangerous -[no]v bool no Be slightly more verbose in messages -posrefc real 1000Force constant for position restraints -vsite enum noneConvert atoms to virtual sites: none, hydrogens or aromatics -[no]heavyh bool no Make hydrogen atoms heavy -[no]deuterate bool no Change the mass of hydrogens to 2 amu -[no]chargegrp bool yes Use charge groups in the rtp file -[no]cmap bool yes Use cmap torsions (if enabled in the rtp file) -[no]renum bool no Renumber the residues consecutively in the output -[no]rtpres bool no Use rtp entry names as residue names Select the Force Field: From current directory: 1: GROMOS96 53A6 force field, extended to include Berger lipid parameters From '/usr/remote/gromacs/4.5.3/share/gromacs/top': 2: AMBER03 force field (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003) 3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995) 4: AMBER96 force field (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996) 5: AMBER99 force
[gmx-users] cannot rename checkpoint file
Dear Gromacs users, I am running an all-atom simulation of protein-ligand complex in lipid bilayer on a server, while running the job after some time, my job terminates with an error as under: Program mdrun, VERSION 4.0.3 Source code file: checkpoint.c, line: 859 File input/output error: Cannot rename checkpoint file; maybe you are out of quota? Please suggest how to overcome this error. Best, Ram -- 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] cannot rename checkpoint file
ram bio wrote: Dear Gromacs users, I am running an all-atom simulation of protein-ligand complex in lipid bilayer on a server, while running the job after some time, my job terminates with an error as under: Program mdrun, VERSION 4.0.3 Source code file: checkpoint.c, line: 859 File input/output error: Cannot rename checkpoint file; maybe you are out of quota? Please suggest how to overcome this error. The error suggests you are out of disk space. Is this the case? Otherwise, I'd suggest upgrading your Gromacs version. Dozens of bugs have been fixed. -Justin Best, Ram -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] amber96 RB dihedrals in GMX 4.0 and 4.5
Hello Context: I have prepared the same system (WW domain) with GMX 4.0.7 and 4.5.3 using amber96. Doing a gmxdump on the tpr files seems to show that the RB dihedrals are absent from the 4.5-prepared system, but present in the 4.0-prepared one. I used the same mdp files for both GMX versions. gmxdump -s system.tpr | grep RBDI Looking at the [dihedrals] directive in the topology file: 4.0 has funct 1 (proper dihedrals) and funct 3 (RB dihedrals) while 4.5 has funct 4 (improper) and funct 9 (proper) (pages 108 and 124 for the 4.0 and 4.5 respectively). The 4.5 manual (page 129 under the [dihedrals] directive description) seems to imply that the RB dihedrals need to be added by hand and the 1-4 interaction in [pairs] should be removed for the atoms involved in the RB dihedrals. Is this correct? Question: What is the best way to prepare a system with Ryckaert-Bellemans dihedrals in GMX 4.5? Thanks for your time. -- Badi' Abdul-Wahid -- 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: Secondary structure loss in implicit solvent simulations
Do you get the same effects if you run a normal simulation on CPU and not GPU? That information would be critical for properly diagnosing what's going on. If it's not GPU-specific, in all likelihood whatever you're doing is incorrect somewhere along the way. Folllowing up on this -- if it's not the same trajectory as the CPU to within single precision, then something is wrong. So the energies should be the same to 5 digits for the first time steps, and then gradually drift away. If it's not the same for the first 5-10 steps, then there is something going wrong with the GPU code or the setup for the GPU code. -- 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] GPU gets faster with more molecules in system
Hi, I compiled mdrun-gpu and tried some waterbox systems with different atoms counts. atoms | GPU| CPU 2.400 | 1.015s | 774s 4.800 | 1.225s | 1.202s 9.600 | 1.142s | 1.353s 19.200 | 2.984s | 2.812s Why does the system with 9.600 atoms finish faster than the one with 4.800? I tripple checked the simualtions and even GROMACs tells me that the atom count in the system is like above. So I think no mistaken there. A diff of md.log only shows differences in output values for each step. Is there any explanation for this behaviour? Christian -- 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] GPU gets faster with more molecules in system
On 25/01/2011 8:25 AM, Christian Mötzing wrote: Hi, I compiled mdrun-gpu and tried some waterbox systems with different atoms counts. atoms | GPU| CPU 2.400 | 1.015s | 774s 4.800 | 1.225s | 1.202s 9.600 | 1.142s | 1.353s 19.200 | 2.984s | 2.812s Why does the system with 9.600 atoms finish faster than the one with 4.800? I tripple checked the simualtions and even GROMACs tells me that the atom count in the system is like above. So I think no mistaken there. A diff of md.log only shows differences in output values for each step. Is there any explanation for this behaviour? As a guess, the cost of overheads for molecular simulations tend to have a weaker dependence on system size than the cost of computation (or none at all). Only once the latter dominate the cost do you see scaling with system size. I expect you'd see similar behaviour running systems with 64, 128, 256, 512 atoms on 64 processors. 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
Re: [gmx-users] amber96 RB dihedrals in GMX 4.0 and 4.5
On 25/01/2011 4:53 AM, Badi' Abdul-Wahid wrote: Hello Context: I have prepared the same system (WW domain) with GMX 4.0.7 and 4.5.3 using amber96. Doing a gmxdump on the tpr files seems to show that the RB dihedrals are absent from the 4.5-prepared system, but present in the 4.0-prepared one. I used the same mdp files for both GMX versions. gmxdump -s system.tpr | grep RBDI Looking at the [dihedrals] directive in the topology file: 4.0 has funct 1 (proper dihedrals) and funct 3 (RB dihedrals) while 4.5 has funct 4 (improper) and funct 9 (proper) (pages 108 and 124 for the 4.0 and 4.5 respectively). Building AMBER topologies requires that the residue database have the ability to add up multiple instances of type 1 dihedrals, which is an ability that was lacking in 4.0. Type 9 was introduced in 4.5 to deal with this and similar situations. Under some circumstances, multiple type 1 dihedrals can be combined into an R-B dihedral, and this was the work-around in 4.0. Function type 9 avoids this need. You should find that each produces the same energy in a zero-step MD. I would have expected the improper dihedral treatment in each GROMACS version to be the same. The 4.5 manual (page 129 under the [dihedrals] directive description) seems to imply that the RB dihedrals need to be added by hand and the 1-4 interaction in [pairs] should be removed for the atoms involved in the RB dihedrals. Is this correct? I think not. This is force-field- and system-specific. See 4.2.12. Question: What is the best way to prepare a system with Ryckaert-Bellemans dihedrals in GMX 4.5? I think you should have no need to use them with amber96. 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
[gmx-users] mdrun_mpi executable not found
Dear gmx users, I have installed the parallel version 4.0.7 of gromacs on one of the nodes of my cluster. Here is the steps I've done through root: first, the normal installation: ./configure make make install make links then issued commands below for the mpi build: ./configure --enable-mpi make mdrun make install-mdrun make links I dont see any errors and everything seems to install fine. I then switch to a normal user to do my work and then after issuing the grompp_md command as usual, I entered the command below: mpirun -np 8 mdrun_mpi -s *.tpr -o *.tpr -c *_after_md -v output.mdrun_md however, output.mdrun_md gives: mpirun was unable to launch the specified application as it could not find an executable: Executable: mdrun_mpi Node: node3.reyclus.loc while attempting to start process rank 0. Was the installation procedure incorrect? Or do I need to go through a separate installation for the mdrun_mpi executable? Please guide me on what is wrong. Thanks, Justin -- 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] mdrun_mpi executable not found
Justin Kat wrote: Dear gmx users, I have installed the parallel version 4.0.7 of gromacs on one of the nodes of my cluster. Here is the steps I've done through root: first, the normal installation: ./configure make make install make links then issued commands below for the mpi build: ./configure |--enable-mpi| make mdrun make install-mdrun make links I dont see any errors and everything seems to install fine. I then switch to a normal user to do my work and then after issuing the grompp_md command as usual, I entered the command below: mpirun -np 8 mdrun_mpi -s *.tpr -o *.tpr -c *_after_md -v output.mdrun_md however, output.mdrun_md gives: mpirun was unable to launch the specified application as it could not find an executable: Executable: mdrun_mpi Node: node3.reyclus.loc while attempting to start process rank 0. Was the installation procedure incorrect? Or do I need to go through a separate installation for the mdrun_mpi executable? Please guide me on what is wrong. No, the commands you gave should have built mdrun_mpi, as long as they finished successfully. Were there errors in the installation? With make links you should have links to all the Gromacs executables in /usr/local/bin - are they there? You don't need to make links, instead you can follow the steps here: http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation -Justin Thanks, Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] using Berger Lipids in gromacs 4.5.3
The issue is in atomtypes.atp and is related to an open issue: http://redmine.gromacs.org/issues/618 Something is wrong with the way atomtypes.atp is handled, such that if any change is made to it, pdb2gmx either hangs or assigns the wrong atom types. There is no need to modify the .atp file for the force field. Deleting the lines you added (and the blank at the end of the file, which in and of itself causes a hang) fixes the problem. -Justin NG HUI WEN wrote: Sorry! Was quite sure I had them attached... Thanks again!! Huiwen -Original Message- From: Justin A. Lemkul [mailto:jalem...@vt.edu] Sent: Tuesday, January 25, 2011 8:27 AM To: NG HUI WEN Subject: Re: [gmx-users] using Berger Lipids in gromacs 4.5.3 There is no attachment. -Justin NG HUI WEN wrote: Hi Justin, Here are the files for you. Many thanks for your help in advance! Let me know if you need anything else. Huiwen -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul Sent: Mon 1/24/2011 10:48 PM To: Gromacs Users' List Subject: Re: [gmx-users] using Berger Lipids in gromacs 4.5.3 NG HUI WEN wrote: Hi Justin, Thanks for your reply. I am using linux on a cluster remotely. It is made up of Hewlett Packard ProLiant DL160 compute nodes. I didn't see any ._ appearing in my gromos53a6_lipid.ff folder. Can you send me a tarball of your gromos53a6_lipid.ff folder (off-list) so I can try to troubleshoot this? Your input .pdb file would be useful, as well. -Justin Huiwen -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Monday, January 24, 2011 10:14 PM To: Gromacs Users' List Subject: Re: [gmx-users] using Berger Lipids in gromacs 4.5.3 NG HUI WEN wrote: Dear Justin, Thanks for pointing out :) much appreciated. I tried selecting 1 and the process seemed to stop after the work Atomtype 1, please see below: pdb2gmx -f prot_moved.pdb -o prot_pdb2gmx.pdb -p prot.top -ter -asp -his :-) G R O M A C S (-: GROningen MAchine for Chemical Simulation :-) VERSION 4.5.3 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) pdb2gmx (-: Option Filename Type Description -f prot_moved.pdb InputStructure file: gro g96 pdb tpr etc. -o prot_pdb2gmx.pdb Output Structure file: gro g96 pdb etc. -p prot.top Output Topology file -i posre.itp Output Include file for topology -n clean.ndx Output, Opt. Index file -q clean.pdb Output, Opt. Structure file: gro g96 pdb etc. Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint0 Set the nicelevel -chainsep enum id_or_ter Condition in PDB files when a new chain and molecule_type should be started: id_or_ter, id_and_ter, ter, id or interactive -ff string select Force field, interactive by default. Use -h for information. -water enum select Water model to use: select, none, spc, spce, tip3p, tip4p or tip5p -[no]inter bool no Set the next 8 options to interactive -[no]ss bool no Interactive SS bridge selection -[no]ter bool yes Interactive termini selection, iso charged -[no]lys bool no Interactive Lysine selection, iso charged -[no]arg bool no Interactive Arganine selection, iso charged -[no]asp bool yes Interactive Aspartic Acid selection, iso charged -[no]glu bool no Interactive Glutamic Acid selection, iso charged -[no]gln bool no Interactive Glutamine selection, iso neutral -[no]his bool yes Interactive Histidine selection, iso checking H-bonds -angle real 135 Minimum hydrogen-donor-acceptor angle for a H-bond (degrees) -distreal 0.3 Maximum donor-acceptor distance for a H-bond (nm) -[no]una bool no Select aromatic rings with united CH atoms on Phenylalanine, Tryptophane and Tyrosine -[no]ignhbool no Ignore hydrogen
Re: [gmx-users] mdrun_mpi executable not found
Thank you for the reply! hmm mdrun_mpi does not appear in the list of executables in /usr/local/gromacs/bin (and well therefore not in /usr/local/bin). Which set of installation commands that I used should have compiled the mdrun_mpi executable? And how should I go about getting the mdrun_mpi executable at this point? Justin On Mon, Jan 24, 2011 at 6:57 PM, Justin A. Lemkul jalem...@vt.edu wrote: Justin Kat wrote: Dear gmx users, I have installed the parallel version 4.0.7 of gromacs on one of the nodes of my cluster. Here is the steps I've done through root: first, the normal installation: ./configure make make install make links then issued commands below for the mpi build: ./configure |--enable-mpi| make mdrun make install-mdrun make links I dont see any errors and everything seems to install fine. I then switch to a normal user to do my work and then after issuing the grompp_md command as usual, I entered the command below: mpirun -np 8 mdrun_mpi -s *.tpr -o *.tpr -c *_after_md -v output.mdrun_md however, output.mdrun_md gives: mpirun was unable to launch the specified application as it could not find an executable: Executable: mdrun_mpi Node: node3.reyclus.loc while attempting to start process rank 0. Was the installation procedure incorrect? Or do I need to go through a separate installation for the mdrun_mpi executable? Please guide me on what is wrong. No, the commands you gave should have built mdrun_mpi, as long as they finished successfully. Were there errors in the installation? With make links you should have links to all the Gromacs executables in /usr/local/bin - are they there? You don't need to make links, instead you can follow the steps here: http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation -Justin Thanks, Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
RE: [gmx-users] using Berger Lipids in gromacs 4.5.3
It worked! Thanks very much again for your time and help. Cheers, huiwen -Original Message- From: Justin A. Lemkul [mailto:jalem...@vt.edu] Sent: Tuesday, January 25, 2011 8:49 AM To: NG HUI WEN; Gromacs Users' List Subject: Re: [gmx-users] using Berger Lipids in gromacs 4.5.3 The issue is in atomtypes.atp and is related to an open issue: http://redmine.gromacs.org/issues/618 Something is wrong with the way atomtypes.atp is handled, such that if any change is made to it, pdb2gmx either hangs or assigns the wrong atom types. There is no need to modify the .atp file for the force field. Deleting the lines you added (and the blank at the end of the file, which in and of itself causes a hang) fixes the problem. -Justin NG HUI WEN wrote: Sorry! Was quite sure I had them attached... Thanks again!! Huiwen -Original Message- From: Justin A. Lemkul [mailto:jalem...@vt.edu] Sent: Tuesday, January 25, 2011 8:27 AM To: NG HUI WEN Subject: Re: [gmx-users] using Berger Lipids in gromacs 4.5.3 There is no attachment. -Justin NG HUI WEN wrote: Hi Justin, Here are the files for you. Many thanks for your help in advance! Let me know if you need anything else. Huiwen -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul Sent: Mon 1/24/2011 10:48 PM To: Gromacs Users' List Subject: Re: [gmx-users] using Berger Lipids in gromacs 4.5.3 NG HUI WEN wrote: Hi Justin, Thanks for your reply. I am using linux on a cluster remotely. It is made up of Hewlett Packard ProLiant DL160 compute nodes. I didn't see any ._ appearing in my gromos53a6_lipid.ff folder. Can you send me a tarball of your gromos53a6_lipid.ff folder (off-list) so I can try to troubleshoot this? Your input .pdb file would be useful, as well. -Justin Huiwen -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Monday, January 24, 2011 10:14 PM To: Gromacs Users' List Subject: Re: [gmx-users] using Berger Lipids in gromacs 4.5.3 NG HUI WEN wrote: Dear Justin, Thanks for pointing out :) much appreciated. I tried selecting 1 and the process seemed to stop after the work Atomtype 1, please see below: pdb2gmx -f prot_moved.pdb -o prot_pdb2gmx.pdb -p prot.top -ter -asp -his :-) G R O M A C S (-: GROningen MAchine for Chemical Simulation :-) VERSION 4.5.3 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) pdb2gmx (-: Option Filename Type Description -f prot_moved.pdb InputStructure file: gro g96 pdb tpr etc. -o prot_pdb2gmx.pdb Output Structure file: gro g96 pdb etc. -p prot.top Output Topology file -i posre.itp Output Include file for topology -n clean.ndx Output, Opt. Index file -q clean.pdb Output, Opt. Structure file: gro g96 pdb etc. Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint0 Set the nicelevel -chainsep enum id_or_ter Condition in PDB files when a new chain and molecule_type should be started: id_or_ter, id_and_ter, ter, id or interactive -ff string select Force field, interactive by default. Use -h for information. -water enum select Water model to use: select, none, spc, spce, tip3p, tip4p or tip5p -[no]inter bool no Set the next 8 options to interactive -[no]ss bool no Interactive SS bridge selection -[no]ter bool yes Interactive termini selection, iso charged -[no]lys bool no Interactive Lysine selection, iso charged -[no]arg bool no Interactive Arganine selection, iso charged -[no]asp bool yes Interactive Aspartic Acid selection, iso charged -[no]glu bool no Interactive Glutamic Acid selection, iso charged -[no]gln bool no Interactive Glutamine selection, iso neutral -[no]his bool yes Interactive
Re: [gmx-users] mdrun_mpi executable not found
Justin Kat wrote: Thank you for the reply! hmm mdrun_mpi does not appear in the list of executables in /usr/local/gromacs/bin (and well therefore not in /usr/local/bin). Which set of installation commands that I used should have compiled the mdrun_mpi executable? And how should I go about getting the mdrun_mpi executable at this point? I see it now. When you configured with --enable-mpi, you didn't specify --program-suffix=_mpi, so the installation procedure over-wrote your existing (serial) mdrun with an MPI-enabled one simply called mdrun. The configure output should have warned you about this. You could, in theory, simply re-name your existing executable mdrun_mpi and then re-install a serial mdrun, if you need it. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Need help troubleshooting an mdrun-gpu error message!
Hello friends, I have installed mdrun-gpu v. 4.5.3 without incident on my group's computer with a suitable GPU. The computer uses a Linux OS. CUDA and OpenMM are installed in the usual places. I created the topol.tpr file with grompp v. 4.5.3, also without incident. When I run ./mdrun-gpu -v, the following error message is produced: Program mdrun-gpu, VERSION 4.5.3 Source code file: /home/smberman/sourcecode/gromacs-4.5.3/src/kernel/openmm_wrapper.cpp, line: 1259 Fatal error: The requested platform CUDA could not be found. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I have the following in my .bash_profile: export PATH=~/bin:~/usr/bin:~/usr/local/bin:/usr/local/cuda/bin:$PATH:. LD_LIBRARY_PATH=/usr/local/openmm/lib:/usr/local/cuda/lib export LD_LIBRARY_PATH I have run the available tests that came with the OpenMM library, and the CUDA tests pass. Could someone please explain what this error means and the appropriate way to remedy it? Thank you!! Best, Solomon Berman Chemistry Department Boston University -- 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
