Re: [gmx-users] simulating copper nano particles
abhishek sharma wrote: dear all, I am simulating four copper nanoparticles places symetrically so that their centres form a regular tetrahederon.I am trying understand their sintering behavior.So is their any method to calculate the position of centre of maas of the whole system at any time (say t) as all the particles moves causing shift in the centre of maas.!! abhishek ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php g_traj -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Coordinates in hdel.top and hdel.gro not matching
Dear gmx-users, I am trying to simulate protein-DNA complex and i am using AMBER port for ForceField. I have edited my PDB and spc.itp to suit parameters. While preprocessing the following error is shown. The number of atoms in .top and .gro files are not matching. It is not taking into account the number of solvent molecule (74040) which are added during the genbox. I tried summing up water (391) in PDB and solvating water (74040) in a single line in hdel.top. Then it shows error difference in atom (391+74040). Back Off! I just backed up mdout.mdp to ./#mdout.mdp.11# checking input for internal consistency... calling /lib/cpp -traditional... Tried to execute: '/lib/cpp -traditional -I/usr/local/gromacs/share/top -D_FF_A MBER2 hdel.top > grompp1LWQAw' The '/lib/cpp -traditional' command is defined in the .mdp file processing topology... Generated 2628 of the 2628 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2628 of the 2628 1-4 parameter combinations Excluding 3 bonded neighbours for Protein_A 1 Excluding 3 bonded neighbours for Protein_B 1 Excluding 3 bonded neighbours for Protein_5 1 Excluding 3 bonded neighbours for Protein_C 1 Excluding 3 bonded neighbours for Protein_3 1 Excluding 3 bonded neighbours for Protein_D 1 Excluding 2 bonded neighbours for SOL 391 Excluding 2 bonded neighbours for SOL 74040 WARNING 1 [file "hdel.top", line 47]: System has non-zero total charge: -1.502655e+02 processing coordinates... Fatal error: number of coordinates in coordinate file (hdel.gro, 302737) does not match topology (hdel.top, 228697) Is this error due to charge ? In this case i am unable to use genion as it needs .tpr generated by grompp. how the coordinates are not matching. Is last line of .top file is not read. Thanks and regards ALAGURAJ VELUCHAMY c/o Dr.S.KRISHNASWAMY, CENTRE OF EXCELLENCE IN BIOINFORMATICS, MADURAI KAMARAJ UNIVERSITY, MADURAI, TN. Ph:09486148690 - Bored stiff? Loosen up... Download and play hundreds of games for free on Yahoo! Games.___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] simulating copper nano particles
abhishek sharma wrote: dear all, I am simulating four copper nanoparticles places symetrically so that their centres form a regular tetrahederon.I am trying understand their sintering behavior.So is their any method to calculate the position of centre of maas of the whole system at any time (say t) as all the particles moves causing shift in the centre of maas.!! abhishek Yup... the same way they teach first-year physics students to calculate the centre of mass. See http://en.wikipedia.org/wiki/Center_of_mass#Definition I doubt there's any gromacs analysis tool already written to do this, however, so you'd have to write a script, or program, or Excel spreadsheet to do it. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] simulating copper nano particles
dear all, I am simulating four copper nanoparticles places symetrically so that their centres form a regular tetrahederon.I am trying understand their sintering behavior.So is their any method to calculate the position of centre of maas of the whole system at any time (say t) as all the particles moves causing shift in the centre of maas.!! abhishek ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RE: Regarding membrane protein solvation
Dear Alan Dodd, Thank you for your suggestion. with regards, Nagaraju - You snooze, you lose. Get messages ASAP with AutoCheck in the all-new Yahoo! Mail Beta. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] simulation
abhishek sharma wrote: i am simulating four nanoparticles having samr radii places in a tertahederal manner.i want to calculate the shift in the centre of each sphere during their motion.is their any method to calculate the position of centre of any sphere after any time (say t) Please use normal English spelling and capitalization. Anything you can do that makes your message more appealing to read makes it more likely that people will want to read it and thus help you. The answer to your question is "yes", but you'll need to be more descriptive to get a useful answer... Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] simulation
i am simulating four nanoparticles having samr radii places in a tertahederal manner.i want to calculate the shift in the centre of each sphere during their motion.is their any method to calculate the position of centre of any sphere after any time (say t) abhishek ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Walls & table-based potentials
Hello everyone, I am trying to use the new walls feature in the CVS version of gromacs. My system is a simple box of SPC water. When using wall_type: 9-3 or wall_type: 10-4 with appropriate atomtype and density parameters, I have no problems, and the runs proceed normally. However, when I try to use wall_type: table I obtain segmentation faults from the md_run program. These faults only occur when an atom of my simulation crosses into the table-lookup area, within 2nm of one of the walls. So I can postpone the fault by adding 2nm or more of vacuum on either side of my simulation box, but as soon as a water molecule escapes, the program crashes. I have tried changing the timestep, temperature, and pressure coupling with no success. I have also tried several different tables: the original table with the potential I am trying to use, the various table6-*.xvg tables from the /top directory, appropriately renamed, as well as a blank table, containing only zeros in all but the first, index, column. All of them fail in precisely the same fashion. Have you any advice on what could be causing this problem? I presume it must be related to the table itself, but I am at a loss as to how to fix it. Thank you all kindly, Brett Olsen ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] web page error on "Downloads Home » Contributed software"
because of recent hacker activity I made all files read-only. Is there something that doesn't work now? Nope. Everything works fine AFAIK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [Fwd: Re: [gmx-users] QMMM free energy]
Gerrit and David, David wrote: But wouldn't BAR work just fine? And On 5/31/07, Gerrit Groenhof <[EMAIL PROTECTED]> wrote: Hi Fiske, From what I understand, you want to compute the free energy for changing one or more atoms in the QM subsystem. I never considered doing this because I do not expect to get sufficient sampling. But in my opinion this should be possible. In case only atoms in the QM subsystem change it is straightforward. But I might overlook something important (maybe someone can comment on this if I make a mistake). I think you should modify the code, so that there are two QM/MM computations per step. Once in the A state and once in the B state, which gives VA and VB. From that you can compute V(lambda) = lamda VB + (1-lambda) VA. And dv/dl = VB-VA. This is then the QM and coulombic QM/MM contribution to dv/dlambda. The lennerd jones should work automatically. But this works only if you are not modifying the charges of the MM atoms. Then things get more messy. However, there is a problem with neighbour searching. Right now, the QM/MM neighbour list is constructed only in the if (!bFreeEnergy) branch of the put_in_list function. I think this is why mdrun crashes. the qmmm interface expects to find MM neighbours, but the QMMM nblists are not created. You can copy the if(bQMMM) branch into the free energy branch. Best, Gerrit Both of you guys are thinking linear mixing of the two Hamiltonia, where one can just evaluate the energies of the end states (lambda=0 and lambda=1) and then combine to get the potential (or dV/dlambda) at the intermediate lambda values. That's fine as far as it goes -- but it won't work for doing insertion/deletion of atoms, where one needs to use something like soft core potentials. Unless I'm missing something obvious, it's not at all clear to me how one would do insertion/deletion of atoms using soft core potentials with QM/MM. Though I don't know much about QM/MM, I do know it involves doing some sort of QM calculation -- and I don't get how that could possibly work with something like soft core potentials, since the QM calculation must use an atom type. If you're deleting an atom, you want, at lambda=0.5, say, an atom that is halfway between a dummy atom and what it originally was (say, a carbon). I have no idea how you'd describe that quantum mechanically. And as far as whether BAR would save the day... Nope. You need to have the potential energy of your snapshots evaluated at different lambda values as input for BAR, which means you have to figure out how to evaluate a QM energy for an atom that is halfway between a dummy atom and a carbon atom. I don't get how this would work. Maybe someone has worked this out already -- again, I'd look at what Wei Yang, or anyone else doing QM/MM free energy calculations, is doing. But it's definitely not something that's immediately obvious. David > > Subject: > Re: [gmx-users] QMMM free energy > From: > Erik Lindahl <[EMAIL PROTECTED]> > Date: > Wed, 30 May 2007 17:34:59 +0200 > To: > Discussion list for GROMACS users > > To: > Discussion list for GROMACS users > > > Hi, > > I'm not a QM expert myself (Gerrit, comments?), but I'm pretty sure > the main reason is that you cannot either mutate atom types or > decouple interactions gradually in the QM part of the system. Once > this is solved for a pure QM system it should be straightforward to > implement the QM/MM interface of it. > > Cheers, > > Erik > > On May 30, 2007, at 5:30 PM, Robert fiske wrote: > >>> With the original QM/MM implementation, free energy is currently not >>> possible (yet). From what you report, I guess that also with the >>> CPMD interface it does not work. >> >> The CPMD interface is mostly plugged into the same setup as the other >> QM interfaces, I was able to bypass the error by copying modifying >> the free energy else statement to bypass the vdw calculations for the >> case of bQMMM true (and generally try to have that code match the >> bQMMM case of non free energy runs). But since my background is >> Computer Engineering and not chemistry (Chemistry 101 is as far as I >> got in formal training) I don't really know what should be done (I >> assume since as you said it's not implemented yet although I don't >> get a run time error that the results will be off). >> >> Are QM/MM free energy calculations substantially different than MM >> calculations, or is it just not implemented because no one has needed >> to do QM/MM with free energy yet? >> >> >> fiske >> Gogonea Group >> Cleveland State University >> >> _ >> More photos, more messages, more storage—get 2GB with Windows Live >> Hotmail. >> http://imagine-windowslive.com/hotmail/?locale=en-us&ocid=TXT_TAGHM_migration_HM_mini_2G_0507 >> >> >> ___ >> gmx-users mailing listgmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please
Re: [gmx-users] combination rules
priyanka srivastava wrote: Dear All, I would be really thankful if somebody could tell me the combination rules used for creating the [pairtypes] in lipid.itp (i.e. the 1,4 interactions) in GROMOS96. Is it the same as is used in GROMOS87? Does the chapter five of GROMACS manual not describe this? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] combination rules
Dear All, I would be really thankful if somebody could tell me the combination rules used for creating the [pairtypes] in lipid.itp (i.e. the 1,4 interactions) in GROMOS96. Is it the same as is used in GROMOS87? eagerly waiting for the reply, regards, Pri... Pinpoint customers who are looking for what you sell. http://searchmarketing.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] protein-DNA simulation with Amber port
Figured it out was just being a bit slow. I hadn't include an #ifdef _FF_AMBER statement in spce.itp or spc.itp Thanks Erik and Mark Tom --On Friday, June 01, 2007 23:35:22 +1000 Mark Abraham <[EMAIL PROTECTED]> wrote: TJ Piggot wrote: Hi I have just checked again by trying to set up a run again using spc/e with amber03. I still get this same error. I am sure the order in the [ molecules ] section is correct, and it is the same order as in the .top file with tip3p or tip4p which both work fine. The only difference between the setup's is the -water option given to pdb2gmx and the -cs option in genbox How do the contents of the water .itp files differ? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] protein-DNA simulation with Amber port
TJ Piggot wrote: Hi I have just checked again by trying to set up a run again using spc/e with amber03. I still get this same error. I am sure the order in the [ molecules ] section is correct, and it is the same order as in the .top file with tip3p or tip4p which both work fine. The only difference between the setup's is the -water option given to pdb2gmx and the -cs option in genbox How do the contents of the water .itp files differ? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] protein-DNA simulation with Amber port
Hi I have just checked again by trying to set up a run again using spc/e with amber03. I still get this same error. I am sure the order in the [ molecules ] section is correct, and it is the same order as in the .top file with tip3p or tip4p which both work fine. The only difference between the setup's is the -water option given to pdb2gmx and the -cs option in genbox Tom --On Friday, June 01, 2007 14:59:53 +0200 Erik Marklund <[EMAIL PROTECTED]> wrote: spc/e works fine for me with ffAMBER03. Are you sure the ordering of your top-file is correct? Check that the [ molecules ] section in correctly ordered. 1 jun 2007 kl. 14.55 skrev TJ Piggot: Hi, If i remember correctly i also got this error with spc (and spc/e) and the ffamber port. However i was only playing around in testing different water models and did not spend ages trying to fix this problem because i use tip3p or tip4p for most of my runs. So as to the error i am not sure, however if you try one of the tip*p water models i think that you should not get this error (remember to have #include ffamber_tip*p in your .top file). Sorry i can't be of more help Tom --On Friday, June 01, 2007 01:25:22 -0700 Alaguraj Veluchamy <[EMAIL PROTECTED]> wrote: Dear Gmx-users, I have followed http://folding.stanford.edu/ffamber/ for porting amber in Gromacs and i am trying to simulate protein-DNA complex. Preprocessing the topology files gives error as below: Back Off! I just backed up mdout.mdp to ./#mdout.mdp.22# checking input for internal consistency... calling /lib/cpp -traditional... processing topology... Generated 2628 of the 2628 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2628 of the 2628 1-4 parameter combinations Cleaning up temporary file gromppkzsTQq Fatal error: [ file "/usr/local/gromacs/share/top/spc.itp", line 41 ]: Atom index (1) in settles out of bounds (1-0) I checked at the spc.itp file and found that the line 41 is: [ settles ] ; OWfunct doh dhh 1 1 0.1 0.16333 and i am using em.mdp file: ; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; cpp = /lib/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 100 ; ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel = no I tried the earlier post suggestion: that "include spc.itp " line must be before the "[molecule] section", but still gives the same error as: Fatal error: [ file "/usr/local/gromacs/share/top/spc.itp", line 41 ]: Atom index (1) in settles out of bounds (1-0) Thanks and regards -Alaguraj.V ALAGURAJ VELUCHAMY c/o Dr.S.KRISHNASWAMY, CENTRE OF EXCELLENCE IN BIOINFORMATICS, MADURAI KAMARAJ UNIVERSITY, MADURAI, TN. Ph:09486148690 __ Never miss an email again! Yahoo! Toolbar alerts you the instant new Mail arrives. Check it out. -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 [EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] OT: script to mutate residues
Am Freitag, 1. Juni 2007 14:56:58 schrieb Erik Marklund: > You can script pymol. Something like pymol -c -q mutation_script.pml. ah, completly forgot about that... ... I'll give this a try... Thanks Martin ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] protein-DNA simulation with Amber port
spc/e works fine for me with ffAMBER03. Are you sure the ordering of your top-file is correct? Check that the [ molecules ] section in correctly ordered. 1 jun 2007 kl. 14.55 skrev TJ Piggot: Hi, If i remember correctly i also got this error with spc (and spc/e) and the ffamber port. However i was only playing around in testing different water models and did not spend ages trying to fix this problem because i use tip3p or tip4p for most of my runs. So as to the error i am not sure, however if you try one of the tip*p water models i think that you should not get this error (remember to have #include ffamber_tip*p in your .top file). Sorry i can't be of more help Tom --On Friday, June 01, 2007 01:25:22 -0700 Alaguraj Veluchamy <[EMAIL PROTECTED]> wrote: Dear Gmx-users, I have followed http://folding.stanford.edu/ffamber/ for porting amber in Gromacs and i am trying to simulate protein-DNA complex. Preprocessing the topology files gives error as below: Back Off! I just backed up mdout.mdp to ./#mdout.mdp.22# checking input for internal consistency... calling /lib/cpp -traditional... processing topology... Generated 2628 of the 2628 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2628 of the 2628 1-4 parameter combinations Cleaning up temporary file gromppkzsTQq Fatal error: [ file "/usr/local/gromacs/share/top/spc.itp", line 41 ]: Atom index (1) in settles out of bounds (1-0) I checked at the spc.itp file and found that the line 41 is: [ settles ] ; OWfunct doh dhh 1 1 0.1 0.16333 and i am using em.mdp file: ; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; cpp = /lib/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 100 ; ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel = no I tried the earlier post suggestion: that "include spc.itp " line must be before the "[molecule] section", but still gives the same error as: Fatal error: [ file "/usr/local/gromacs/share/top/spc.itp", line 41 ]: Atom index (1) in settles out of bounds (1-0) Thanks and regards -Alaguraj.V ALAGURAJ VELUCHAMY c/o Dr.S.KRISHNASWAMY, CENTRE OF EXCELLENCE IN BIOINFORMATICS, MADURAI KAMARAJ UNIVERSITY, MADURAI, TN. Ph:09486148690 __ Never miss an email again! Yahoo! Toolbar alerts you the instant new Mail arrives. Check it out. -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 [EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] OT: script to mutate residues
You can script pymol. Something like pymol -c -q mutation_script.pml. /Erik 1 jun 2007 kl. 13.53 skrev Martin Höfling: Hi all, this is slightly OT but maybe someone has already written a quick hack or so: I wanna mutate a residue in a pdb/gro file with an other one (matching to backbone). There are several programs like pymol, swisspdb viewer etc... ... but is there sth. like a script to do this automatically without interactive input? like: mutate --input myprotein.pdb --output mymutated.pdb --resid 12 -- tores K Cheers Martin ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 [EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] protein-DNA simulation with Amber port
Hi, If i remember correctly i also got this error with spc (and spc/e) and the ffamber port. However i was only playing around in testing different water models and did not spend ages trying to fix this problem because i use tip3p or tip4p for most of my runs. So as to the error i am not sure, however if you try one of the tip*p water models i think that you should not get this error (remember to have #include ffamber_tip*p in your .top file). Sorry i can't be of more help Tom --On Friday, June 01, 2007 01:25:22 -0700 Alaguraj Veluchamy <[EMAIL PROTECTED]> wrote: Dear Gmx-users, I have followed http://folding.stanford.edu/ffamber/ for porting amber in Gromacs and i am trying to simulate protein-DNA complex. Preprocessing the topology files gives error as below: Back Off! I just backed up mdout.mdp to ./#mdout.mdp.22# checking input for internal consistency... calling /lib/cpp -traditional... processing topology... Generated 2628 of the 2628 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2628 of the 2628 1-4 parameter combinations Cleaning up temporary file gromppkzsTQq Fatal error: [ file "/usr/local/gromacs/share/top/spc.itp", line 41 ]: Atom index (1) in settles out of bounds (1-0) I checked at the spc.itp file and found that the line 41 is: [ settles ] ; OWfunct doh dhh 1 1 0.1 0.16333 and i am using em.mdp file: ; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; cpp = /lib/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 100 ; ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel = no I tried the earlier post suggestion: that "include spc.itp " line must be before the "[molecule] section", but still gives the same error as: Fatal error: [ file "/usr/local/gromacs/share/top/spc.itp", line 41 ]: Atom index (1) in settles out of bounds (1-0) Thanks and regards -Alaguraj.V ALAGURAJ VELUCHAMY c/o Dr.S.KRISHNASWAMY, CENTRE OF EXCELLENCE IN BIOINFORMATICS, MADURAI KAMARAJ UNIVERSITY, MADURAI, TN. Ph:09486148690 __ Never miss an email again! Yahoo! Toolbar alerts you the instant new Mail arrives. Check it out. -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] OT: script to mutate residues
Hi all, this is slightly OT but maybe someone has already written a quick hack or so: I wanna mutate a residue in a pdb/gro file with an other one (matching to backbone). There are several programs like pymol, swisspdb viewer etc... ... but is there sth. like a script to do this automatically without interactive input? like: mutate --input myprotein.pdb --output mymutated.pdb --resid 12 --tores K Cheers Martin ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Regarding membrane protein solvation
Check the manual for 'genbox'. Once you work out how to use it, remember to check your output for waters within the bilayer - I'm not sure how big the cavities are, but I wouldn't be surprised if you could fit a water molecule or two in. - Original Message From: naga raju <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Friday, June 1, 2007 8:07:08 AM Subject: [gmx-users] Regarding membrane protein solvation Dear gmx users, I inserted mebrane protein in DOPC lipid bilayer, some part of protein is outside of lipid bilayer. Would you tell me how to add water molecules to protein(to the out side of lipid bilayer part) around 6 angstroms radius. any suggestion is appreciated. with best regards, Nagaraja. Get your own web address. Have a HUGE year through Yahoo! Small Business. http://smallbusiness.yahoo.com/domains/?p=BESTDEAL ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Get your own web address. Have a HUGE year through Yahoo! Small Business. http://smallbusiness.yahoo.com/domains/?p=BESTDEAL ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] protein-DNA simulation with Amber port
Dear Gmx-users, I have followed http://folding.stanford.edu/ffamber/ for porting amber in Gromacs and i am trying to simulate protein-DNA complex. Preprocessing the topology files gives error as below: Back Off! I just backed up mdout.mdp to ./#mdout.mdp.22# checking input for internal consistency... calling /lib/cpp -traditional... processing topology... Generated 2628 of the 2628 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2628 of the 2628 1-4 parameter combinations Cleaning up temporary file gromppkzsTQq Fatal error: [ file "/usr/local/gromacs/share/top/spc.itp", line 41 ]: Atom index (1) in settles out of bounds (1-0) I checked at the spc.itp file and found that the line 41 is: [ settles ] ; OWfunct doh dhh 1 1 0.1 0.16333 and i am using em.mdp file: ; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; cpp = /lib/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 100 ; ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel = no I tried the earlier post suggestion: that "include spc.itp " line must be before the "[molecule] section", but still gives the same error as: Fatal error: [ file "/usr/local/gromacs/share/top/spc.itp", line 41 ]: Atom index (1) in settles out of bounds (1-0) Thanks and regards -Alaguraj.V ALAGURAJ VELUCHAMY c/o Dr.S.KRISHNASWAMY, CENTRE OF EXCELLENCE IN BIOINFORMATICS, MADURAI KAMARAJ UNIVERSITY, MADURAI, TN. Ph:09486148690 - Never miss an email again! Yahoo! Toolbar alerts you the instant new Mail arrives. Check it out.___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Regarding membrane protein solvation
Dear gmx users, I inserted mebrane protein in DOPC lipid bilayer, some part of protein is outside of lipid bilayer. Would you tell me how to add water molecules to protein(to the out side of lipid bilayer part) around 6 angstroms radius. any suggestion is appreciated. with best regards, Nagaraja. Get your own web address. Have a HUGE year through Yahoo! Small Business. http://smallbusiness.yahoo.com/domains/?p=BESTDEAL ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
