[gmx-users] pdb2gmx -missing
I do command pdb2gmx but follow warning and error is came up: WARNING: atom H is missing in residue GLY 1 in the pdb file You might need to add atom H to the hydrogen database of residue GLY in the file ff???.hdb (see the manual) Fatal error: There were 1 missing atoms in molecule Protein_A, if you want to use this incomplete topology anyhow, use the option -missing my pdb file is: HETATM1 N GLY A 1 19.949 29.046 10.462 HETATM2 CA GLY A 1 19.485 28.078 9.486 HETATM3 C GLY A 1 20.152 28.247 8.136 HETATM4 O GLY A 1 19.859 29.193 7.405 HETATM5 1H GLY A 1 20.545 29.773 10.181 HETATM6 2HA GLY A 1 19.690 27.084 9.856 HETATM7 2H GLY A 1 20.356 28.562 11.250 HETATM8 3H GLY A 1 19.099 29.546 10.681 HETATM9 1HA GLY A 1 18.415 28.236 9.347 and my ffamber03.hdb of gly is GLY 2 1 1 H N -C CA 2 6 HA CA N C NGLY 2 3 4 H N CA C 2 6 HA CA N C how I add H to hdb file? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] energy minimization - not converge
Hi I want to do energy minimization but follow subject is came up: writing lowest energy coordinates. Back Off! I just backed up ooo.gro to ./#ooo.gro.5# Steepest Descents did not converge to Fmax < 2000 in 101 steps. Potential Energy = -3.2421097e+05 Maximum force = 1.4766100e+04 on atom 1441 Norm of force = 2.5146213e+02 my em.mdp file is: cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = cg 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 changed nsteps to 1000, 2000 and 1. also I changed emtol to 500 but same error came up again. please guide me -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] pdb2gmx -missing
Hi, Try to use -ignh. On Wed, Nov 11, 2009 at 7:09 PM, leila karami wrote: > I do command pdb2gmx but follow warning and error is came up: > > WARNING: atom H is missing in residue GLY 1 in the pdb file > You might need to add atom H to the hydrogen database of residue > GLY > in the file ff???.hdb (see the manual) > > Fatal error: > There were 1 missing atoms in molecule Protein_A, if you want to use this > incomplete topology anyhow, use the option -missing > > my pdb file is: > > HETATM 1 N GLY A 1 19.949 29.046 10.462 > HETATM 2 CA GLY A 1 19.485 28.078 9.486 > HETATM 3 C GLY A 1 20.152 28.247 8.136 > HETATM 4 O GLY A 1 19.859 29.193 7.405 > HETATM 5 1H GLY A 1 20.545 29.773 10.181 > HETATM 6 2HA GLY A 1 19.690 27.084 9.856 > HETATM 7 2H GLY A 1 20.356 28.562 11.250 > HETATM 8 3H GLY A 1 19.099 29.546 10.681 > HETATM 9 1HA GLY A 1 18.415 28.236 9.347 > > and my ffamber03.hdb of gly is > > GLY 2 > 1 1 H N -C CA > 2 6 HA CA N C > > NGLY 2 > 3 4 H N CA C > 2 6 HA CA N C > > how I add H to hdb file? > > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] energy minimization - not converge
Hi Leila, Where does it say that you encountered an error? You also could've checked the wiki/mailing lists for this and found that this is normal and sufficient for starting an MD simulation. Cheers, Tsjerk On Wed, Nov 11, 2009 at 9:10 AM, leila karami wrote: > Hi > > I want to do energy minimization but follow subject is came up: > > writing lowest energy coordinates. > > Back Off! I just backed up ooo.gro to ./#ooo.gro.5# > > Steepest Descents did not converge to Fmax < 2000 in 101 steps. > Potential Energy = -3.2421097e+05 > Maximum force = 1.4766100e+04 on atom 1441 > Norm of force = 2.5146213e+02 > > my em.mdp file is: > > cpp = /usr/bin/cpp > define = -DFLEX_SPC > constraints = none > integrator = cg > 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 changed nsteps to 1000, 2000 and 1. also I changed emtol to 500 but > same error came up again. > please guide me > > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] pdb2gmx -missing
Hi, Well, -ignh is not the right answer here. I recall that just a few days ago someone posted the same problem. For Amber you need to tag the first and last residue. For your GLY, it means you have to rename it to NGLY. Itamar, The warning mentions an atom missing from the .pdb file. These have to be built according to the rules in the .hdb file. The option -ignh is to strip off hydrogen atoms that are present in the .pdb file, but are not listed in the .rtp file and are thus not part of the residue according to the force field. Please make sure that your replies are to the point, because replies that are amiss may confuse the original poster and bring them even further from solving their problems. Cheers, Tsjerk On Wed, Nov 11, 2009 at 9:16 AM, Itamar Kass wrote: > Hi, > > Try to use -ignh. > > On Wed, Nov 11, 2009 at 7:09 PM, leila karami wrote: >> I do command pdb2gmx but follow warning and error is came up: >> >> WARNING: atom H is missing in residue GLY 1 in the pdb file >> You might need to add atom H to the hydrogen database of residue >> GLY >> in the file ff???.hdb (see the manual) >> >> Fatal error: >> There were 1 missing atoms in molecule Protein_A, if you want to use this >> incomplete topology anyhow, use the option -missing >> >> my pdb file is: >> >> HETATM 1 N GLY A 1 19.949 29.046 10.462 >> HETATM 2 CA GLY A 1 19.485 28.078 9.486 >> HETATM 3 C GLY A 1 20.152 28.247 8.136 >> HETATM 4 O GLY A 1 19.859 29.193 7.405 >> HETATM 5 1H GLY A 1 20.545 29.773 10.181 >> HETATM 6 2HA GLY A 1 19.690 27.084 9.856 >> HETATM 7 2H GLY A 1 20.356 28.562 11.250 >> HETATM 8 3H GLY A 1 19.099 29.546 10.681 >> HETATM 9 1HA GLY A 1 18.415 28.236 9.347 >> >> and my ffamber03.hdb of gly is >> >> GLY 2 >> 1 1 H N -C CA >> 2 6 HA CA N C >> >> NGLY 2 >> 3 4 H N CA C >> 2 6 HA CA N C >> >> how I add H to hdb file? >> >> -- >> gmx-users mailing list gmx-us...@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] energy minimization - not converge
leila karami wrote: Hi I want to do energy minimization but follow subject is came up: writing lowest energy coordinates. Back Off! I just backed up ooo.gro to ./#ooo.gro.5# Steepest Descents did not converge to Fmax < 2000 in 101 steps. Potential Energy = -3.2421097e+05 Maximum force = 1.4766100e+04 on atom 1441 Norm of force = 2.5146213e+02 my em.mdp file is: I doubt it - the above output claims the use of integrator = steep and nsteps = 100, unlike the below. Computers and science are very exacting, and you need to be also when you work with both of them! cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = cg 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 changed nsteps to 1000, 2000 and 1. also I changed emtol to 500 but same error came up again. Changing this file won't help - change the correct one. Getting output with the same maximum number of steps was a good hint that you're using the same input... 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] pdb2gmx -missing
Sorry if I made someone more confuse, I thought this was the problem. Probably reading the original post again would have a wise step. Itamar On Wed, Nov 11, 2009 at 7:25 PM, Tsjerk Wassenaar wrote: > Hi, > > Well, -ignh is not the right answer here. I recall that just a few > days ago someone posted the same problem. For Amber you need to tag > the first and last residue. For your GLY, it means you have to rename > it to NGLY. > > Itamar, > > The warning mentions an atom missing from the .pdb file. These have to > be built according to the rules in the .hdb file. The option -ignh is > to strip off hydrogen atoms that are present in the .pdb file, but are > not listed in the .rtp file and are thus not part of the residue > according to the force field. Please make sure that your replies are > to the point, because replies that are amiss may confuse the original > poster and bring them even further from solving their problems. > > Cheers, > > Tsjerk > > On Wed, Nov 11, 2009 at 9:16 AM, Itamar Kass wrote: >> Hi, >> >> Try to use -ignh. >> >> On Wed, Nov 11, 2009 at 7:09 PM, leila karami >> wrote: >>> I do command pdb2gmx but follow warning and error is came up: >>> >>> WARNING: atom H is missing in residue GLY 1 in the pdb file >>> You might need to add atom H to the hydrogen database of residue >>> GLY >>> in the file ff???.hdb (see the manual) >>> >>> Fatal error: >>> There were 1 missing atoms in molecule Protein_A, if you want to use this >>> incomplete topology anyhow, use the option -missing >>> >>> my pdb file is: >>> >>> HETATM 1 N GLY A 1 19.949 29.046 10.462 >>> HETATM 2 CA GLY A 1 19.485 28.078 9.486 >>> HETATM 3 C GLY A 1 20.152 28.247 8.136 >>> HETATM 4 O GLY A 1 19.859 29.193 7.405 >>> HETATM 5 1H GLY A 1 20.545 29.773 10.181 >>> HETATM 6 2HA GLY A 1 19.690 27.084 9.856 >>> HETATM 7 2H GLY A 1 20.356 28.562 11.250 >>> HETATM 8 3H GLY A 1 19.099 29.546 10.681 >>> HETATM 9 1HA GLY A 1 18.415 28.236 9.347 >>> >>> and my ffamber03.hdb of gly is >>> >>> GLY 2 >>> 1 1 H N -C CA >>> 2 6 HA CA N C >>> >>> NGLY 2 >>> 3 4 H N CA C >>> 2 6 HA CA N C >>> >>> how I add H to hdb file? >>> >>> -- >>> gmx-users mailing list gmx-us...@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> -- >> gmx-users mailing list gmx-us...@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > Computational Chemist > Medicinal Chemist > Neuropharmacologist > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Does Gromacs support CHARMM force field now?
xuji wrote: Hi all GMX users: I noticed that there're charmm27 force field files in Gromacs-4.0.5 software package. But charmm27 force field can't be choosed in pdb2gmx. So can I use charmm27 force field in Gromacs now? No. It will be supported as of version 4.1, as has been stated many times over this list (hint: check the archives!) -Justin Thanks for any advice in advance! 2009-11-11 Ji Xu The State Key Laboratory of Multiphase Complex System Institute of Process Engineering Chinese Academy of Sciences Beijing 100190, China Tel.: +86 10 8262 3713-804 ** -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RE: Does Gromacs support CHARMM force field now?
Hi, I noticed that there're charmm27 force field files in Gromacs-4.0.5 software package. But charmm27 force field can't be choosed in pdb2gmx. So can I use charmm27 force field in Gromacs now? The files are there unofficially (that's why they're not included in the ff.dat file) and in an old version. You could try out the charmm27 parameters with CMAP support by downloading the latest version of the source code in git master and use the latest files, which I can provide you with (send an e-mail to me and I'll give them to you). The CHARMM ff (for proteins and lipids at least) will be officially supported in upcoming Gromacs version 4.1. Regards, Pär Bjelkmar-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Increase temperature to 550K
Hi The system = one lysozyme + TIP3P water I was put the system in NTP simulation. Under 550K, all water molecules should evaporate entirely , I suppose ??? >From Justin => "There are plenty of other methodological concerns (pressure coupling especially) " Would you please direct me about this ? Thank you Lin I agree with Mark's earlier comment; the water model alone is not the most immediate concern. A colleague of mine is currently doing lots of high-temperature (up to 600 K) simulations of proteins in TIP3P using the AMBER force fields. There are plenty of other methodological concerns (pressure coupling especially); a thorough search of the literature will give you some insights into what might be wrong. Plenty of groups have successfully been doing high-temperature MD for a number of years. -Justin Chih-Ying Lin wrote: > > Hi > the water model is TIP3P. > > Thanks > Lin > > > > I think the problem is hidden in your water force field model. > > > > The simulation system is merely water + one lysozyme. > > I increase temperate to 550K. > > > > Then, the simulation broke. > > The following message is shown. > > > > MX:hpc0011:Remote endpoint is closed, peer=00:60:dd:48:14:5b (hpc0010:0) > > mpiexec: Warning: task 0 exited with status 1. > > mpiexec: Warning: tasks 1-2 died with signal 9 (Killed). > > mpiexec: Warning: task 3 died with signal 11 (Segmentation fault). > > > > > > Anything wrong with the simulation? > > > > Thank you > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Increase temperature to 550K
Chih-Ying Lin wrote: Hi The system = one lysozyme + TIP3P water I was put the system in NTP simulation. Under 550K, all water molecules should evaporate entirely , I suppose ??? Is this what you want to happen? Are the force field parameters appropriate for such behavior? From Justin => "There are plenty of other methodological concerns (pressure coupling especially) " Would you please direct me about this ? Yes, search the literature. As I said, a number of groups have been doing high-temperature MD for a long time; there are papers out there with methodology you might be able to follow, but since you have not described your goals (are you trying to super-heat a lysozyme solution? improve sampling?) then there is nothing specific to offer. -Justin Thank you Lin I agree with Mark's earlier comment; the water model alone is not the most immediate concern. A colleague of mine is currently doing lots of high-temperature (up to 600 K) simulations of proteins in TIP3P using the AMBER force fields. There are plenty of other methodological concerns (pressure coupling especially); a thorough search of the literature will give you some insights into what might be wrong. Plenty of groups have successfully been doing high-temperature MD for a number of years. -Justin Chih-Ying Lin wrote: Hi the water model is TIP3P. Thanks Lin I think the problem is hidden in your water force field model. > The simulation system is merely water + one lysozyme. > I increase temperate to 550K. > > Then, the simulation broke. > The following message is shown. > > MX:hpc0011:Remote endpoint is closed, peer=00:60:dd:48:14:5b (hpc0010:0) > mpiexec: Warning: task 0 exited with status 1. > mpiexec: Warning: tasks 1-2 died with signal 9 (Killed). > mpiexec: Warning: task 3 died with signal 11 (Segmentation fault). > > > Anything wrong with the simulation? > > Thank you -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Increase temperature to 550K => simulation techniques ?
Hi For running simulaion parameters, people normally not write the details in their papers. high-temperature (up to 600 K) simulations of proteins in TIP3P.. any other detailed suggestion about this ? Thank you Lin I agree with Mark's earlier comment; the water model alone is not the most immediate concern. A colleague of mine is currently doing lots of high-temperature (up to 600 K) simulations of proteins in TIP3P using the AMBER force fields. There are plenty of other methodological concerns (pressure coupling especially); a thorough search of the literature will give you some insights into what might be wrong. Plenty of groups have successfully been doing high-temperature MD for a number of years. -Justin Chih-Ying Lin wrote: > > Hi > the water model is TIP3P. > > Thanks > Lin > > > > I think the problem is hidden in your water force field model. > > > > The simulation system is merely water + one lysozyme. > > I increase temperate to 550K. > > > > Then, the simulation broke. > > The following message is shown. > > > > MX:hpc0011:Remote endpoint is closed, peer=00:60:dd:48:14:5b (hpc0010:0) > > mpiexec: Warning: task 0 exited with status 1. > > mpiexec: Warning: tasks 1-2 died with signal 9 (Killed). > > mpiexec: Warning: task 3 died with signal 11 (Segmentation fault). > > > > > > Anything wrong with the simulation? > > > > Thank you > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Constraints & Restraints
Hi, I just have a quick question on contraints and restraints. My understanding is that "constraints" fix the position of an atom in space and "restraints" restrain the deviation of the atom's position from its equilibrium point. Is that correct? If so, then I am a little confused by the purpose of "constraints = all-bonds" or "constraints = none" in an mdp file, since by selection of a force field, which has bond/angle/dihedral stretching/bending/torsion constants, we are specifying the constraints applied to the simulation. So then what is the purpose of "constraints = all-bonds" and "constraints = none"? Thanks. Darrell -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Constraints & Restraints
darre...@ece.ubc.ca wrote: Hi, I just have a quick question on contraints and restraints. My understanding is that "constraints" fix the position of an atom in space and "restraints" restrain the deviation of the atom's position from its equilibrium point. Is that correct? If so, then I am a little No. A constraint fixes the value of some property (bond length, angle). A restraint indeed biases a certain property (position, distance, dihedral, etc) around some equilibrium value, but it is not strictly fixed. For more, see here: http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints confused by the purpose of "constraints = all-bonds" or "constraints = none" in an mdp file, since by selection of a force field, which has bond/angle/dihedral stretching/bending/torsion constants, we are specifying the constraints applied to the simulation. So then what is the purpose of "constraints = all-bonds" and "constraints = none"? See the LINCS references in the Gromacs manual for detailed descriptions of how constraints are used and what they're doing. -Justin Thanks. Darrell -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Constraints & Restraints
Hi Darrell, Constraints and restraints also apply to relative positions. A bond constraint fixes the bond to a certain distance. constraints = all-bonds means that all bonds are to be converted to constraints, rather than have them flexible, e.g. harmonic. Harmonic bonds are actually more like restraints, penalizing deviations from the equilibrium values. These equilibrium values and the 'penalty function' are described in the force field. Hope it helps, Tsjerk On Wed, Nov 11, 2009 at 9:32 PM, wrote: > > Hi, > I just have a quick question on contraints and restraints. My > understanding is that "constraints" fix the position of an atom in > space and "restraints" restrain the deviation of the atom's position > from its equilibrium point. Is that correct? If so, then I am a little > confused by the purpose of "constraints = all-bonds" or "constraints > = none" in an mdp file, since by selection of a force field, which has > bond/angle/dihedral stretching/bending/torsion constants, we are > specifying the constraints applied to the simulation. So then what is > the purpose of "constraints = all-bonds" and "constraints = none"? > > Thanks. > > Darrell > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] RE: Does Gromacs support CHARMM force field now?
Pär Bjelkmar wrote: Hi, I noticed that there're charmm27 force field files in Gromacs-4.0.5 software package. But charmm27 force field can't be choosed in pdb2gmx. So can I use charmm27 force field in Gromacs now? The files are there unofficially (that's why they're not included in the ff.dat file) and in an old version. You could try out the charmm27 parameters with CMAP support by downloading the latest version of the source code in git master and use the latest files, git actually no longer has anything relevant - Erik took out the files late last month. Mark which I can provide you with (send an e-mail to me and I'll give them to you). The CHARMM ff (for proteins and lipids at least) will be officially supported in upcoming Gromacs version 4.1. Regards, Pär Bjelkmar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] force field: heme group
Dear all, It is known that force field for the heme group doesn't exist in gromacs. So i tried to use amber force fields(AMBER94, AMBER99, AMBER99p, AMBER03, AMBERGS, AMBERGSs) by patching with my latest gromacs version 4.0.5 but still it gives the error message 'Residue 'HEME' not found in residue topology database' Can anyone help me how to solve this problem. Thanks for your help. Rama -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] force field: heme group
No, you're wrong. There are parameters for HEME in several flavours of the GROMOS forcefields, which you can find in the share/gromacs/top/ directory. Ramachandran G skrev: Dear all, It is known that force field for the heme group doesn't exist in gromacs. So i tried to use amber force fields(AMBER94, AMBER99, AMBER99p, AMBER03, AMBERGS, AMBERGSs) by patching with my latest gromacs version 4.0.5 but still it gives the error message 'Residue 'HEME' not found in residue topology database' Can anyone help me how to solve this problem. Thanks for your help. Rama -- --- 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 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Increase temperature to 550K => simulation techniques ?
Chih-Ying Lin wrote: Hi For running simulaion parameters, people normally not write the details in their papers. That's not normally true - the point of a methods section in a paper is that an experienced practitioner in the field could reproduce the work. That is normally much less detailed than an .mdp file, however. high-temperature (up to 600 K) simulations of proteins in TIP3P.. any other detailed suggestion about this ? No, because you didn't take Justin's suggestion. We don't know what your objective is, so we're not going to provide advice (assuming we have any!). Any paper doing high-temperature MD should be defending that choice, and you can follow the references they cite. 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] force field: heme group
Ramachandran G wrote: Dear all, It is known that force field for the heme group doesn't exist in gromacs. So i tried to use amber force fields(AMBER94, AMBER99, That's not true; all of the Gromos variants have heme parameters. AMBER99p, AMBER03, AMBERGS, AMBERGSs) by patching with my latest gromacs version 4.0.5 but still it gives the error message 'Residue 'HEME' not found in residue topology database' Can anyone help me how to solve this problem. Thanks for your help. Well, what is it that you tried? The error message is quite clear - you do not have a [ HEME ] directive in the .rtp file for whatever force field you're trying to use. -Justin Rama -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] force field: heme group
Ramachndran, If you are trying to use the AMBER force field ports for Gromacs (assuming you installed them correctly), I have defined the HEME group for Amber03. If this would help you let me know, and i can provide the files that you need to replace in your gromacs "top" folder -Matt Danielson- // Justin A. Lemkul wrote: Ramachandran G wrote: Dear all, It is known that force field for the heme group doesn't exist in gromacs. So i tried to use amber force fields(AMBER94, AMBER99, That's not true; all of the Gromos variants have heme parameters. AMBER99p, AMBER03, AMBERGS, AMBERGSs) by patching with my latest gromacs version 4.0.5 but still it gives the error message 'Residue 'HEME' not found in residue topology database' Can anyone help me how to solve this problem. Thanks for your help. Well, what is it that you tried? The error message is quite clear - you do not have a [ HEME ] directive in the .rtp file for whatever force field you're trying to use. -Justin Rama -- Matthew L. Danielson Graduate Student of Medicinal Chemistry & Molecular Pharmacology College of Pharmacy, Nursing, and Health Sciences Purdue University MCMP RHPH 504c 575 Stadium Mall Drive West Lafayette, IN 47907-2091 (765)496-3394 office -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] force field: heme group
Matthew L. Danielson wrote: Ramachndran, If you are trying to use the AMBER force field ports for Gromacs (assuming you installed them correctly), I have defined the HEME group for Amber03. If this would help you let me know, and i can provide the files that you need to replace in your gromacs "top" folder This sort of thing would make a nice addition to the "User Contributions" on the Gromacs site, if you're willing to make them widely available to the public :) -Justin -Matt Danielson- // Justin A. Lemkul wrote: Ramachandran G wrote: Dear all, It is known that force field for the heme group doesn't exist in gromacs. So i tried to use amber force fields(AMBER94, AMBER99, That's not true; all of the Gromos variants have heme parameters. AMBER99p, AMBER03, AMBERGS, AMBERGSs) by patching with my latest gromacs version 4.0.5 but still it gives the error message 'Residue 'HEME' not found in residue topology database' Can anyone help me how to solve this problem. Thanks for your help. Well, what is it that you tried? The error message is quite clear - you do not have a [ HEME ] directive in the .rtp file for whatever force field you're trying to use. -Justin Rama -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Constraints & Restraints
Hi Tsjerk, So then, if I understand correctly, setting "constraints = all-bonds" is not as realistic as setting "constraints = none", since the latter will allow for flexible (e.g. harmonic) behavoir which is more realistic than fixing the bond to a certain distance, correct? Thanks. Darrell Date: Wed, 11 Nov 2009 21:45:44 +0100 From: Tsjerk Wassenaar Subject: Re: [gmx-users] Constraints & Restraints To: Discussion list for GROMACS users Message-ID: <8ff89815091245u63c6aa65sa839f24634352...@mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Darrell, Constraints and restraints also apply to relative positions. A bond constraint fixes the bond to a certain distance. constraints = all-bonds means that all bonds are to be converted to constraints, rather than have them flexible, e.g. harmonic. Harmonic bonds are actually more like restraints, penalizing deviations from the equilibrium values. These equilibrium values and the 'penalty function' are described in the force field. Hope it helps, Tsjerk On Wed, Nov 11, 2009 at 9:32 PM, wrote: Hi, I just have a quick question on contraints and restraints. My understanding is that "constraints" fix the position of an atom in space and "restraints" restrain the deviation of the atom's position from its equilibrium point. Is that correct? If so, then I am a little confused by the purpose of "constraints = all-bonds" or "constraints = none" in an mdp file, since by selection of a force field, which has bond/angle/dihedral stretching/bending/torsion constants, we are specifying the constraints applied to the simulation. So then what is the purpose of "constraints = all-bonds" and "constraints = none"? Thanks. Darrell -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Docking with PyMol and using Gromacs
Hi. I am a new user of Gromacs. My question is both PyMol and Gromacs related. I tried the PyMol users mailing list but couldn't find anything. I have a small organic molecule that I am inserting into DNA in pymol. I have the DNA as one pdb file and the organic molecule as another pdb file. I open the DNA file in pymol and then load the organic molecule. After docking the organic molecule I write "save name.pdb" When viewing the name.pdb file in pymol there are some bonds between the organic molecule and the DNA that I don't want. Somehow pymol creates them and I don't see those bonds in the name.pdb file when I open it in a text reader. I then create a .gro file with pdb2gmx of the DNA.pdb and a .gro file of the organic molecule with topolbuilder 1.2 , and unite those .gro files and convert into a .pdb with editconf The newly created pdb file still has those unwanted bonds. My question is: Can I ignore those bonds? If not, how can I prevent pymol making those bonds? 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Adsorption energy of a single molecule
Hi Justin,
So when I create the index file with the molecule and the graphene sheet
and run g_energy, is the adsorption energy between the adsorbed molecule
and the graphene sheet the LJ (SR) energy? And will this energy be just
the interaction energy between the adsorbed molecule and the graphene
sheet (i.e. does the creation of the new index file and executing -rerun
cause g_energy to exclude the energies between the other molecules and
the graphene sheet)?
Thanks.
Darrell
Date: Sun, 01 Nov 2009 21:27:19 -0500
From: "Justin A. Lemkul"
Subject: Re: [gmx-users] Adsorption energy of a single molecule
To: Discussion list for GROMACS users
Message-ID: <4aee4387.40...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Darrell Koskinen wrote:
Hi Justin,
Since I cannot use the original .tpr file, then do I need to run grompp
with the new index file to create a "new" .tpr file, "mdtopolnew.tpr"? I
assume I then need to modify the energygrps line within the .mdp file to
include these new energy groups and then execute "mdrun -rerun
mdtraj.trr -s mdtopolnew.tpr". Is this correct?
Yes, that is the point of the -rerun function.
Does executing "mdrun -rerun mdtraj.trr -s mdtopolnew.tpr" cause a
molecular dynamics simulation to run once again? If so, then will the
exact same molecules that adsorbed on the first MD run be the same ones
that adsorb on the second MD run?
The original coordinates are used to re-calculate the energies. No new
simulation is performed.
-Justin
Thanks.
Darrell
***
***
Date: Sun, 01 Nov 2009 19:29:36 -0500
From: "Justin A. Lemkul"
Subject: Re: [gmx-users] Adsorption energy of a single molecule
To: Discussion list for GROMACS users
Message-ID: <4aee27f0.50...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Darrell Koskinen wrote:
Hi Justin,
In my simulation, I have just over 100 ammonia molecules and, of
these > molecules, 10 to 20 adsorb onto the graphene sheet. I
initially thought > that I would need to tag each one of the ammonia
molecules, since I > would not know, in advance of running the
simulation, which of these > molecules would adsorb.
Are you suggesting that, after the initial simulation run, which
uses an > index file "index.ndx" and is comprised of three components
{System, > Grph, NH3}, I run make_ndx again to assign each adsorbed
molecule to its > own index, execute "mdrun -rerun mdtraj.trr -s
mdtopol.tpr", where > mdtraj.trr and mdtopol.tpr are the output of the
initial simulation, and > then use g_energy to analyze the energies
between the groups?
Almost. You can't use the original .tpr file if you are trying to
establish new energy monitoring groups. Hence the point of making a new
.mdp file. So, re-run the old trajectory with the new .tpr file to take
advantage of the new groups.
-Justin
-- Justin A. Lemkul Ph.D.
Candidate ICTAS Doctoral Scholar 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/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Docking with PyMol and using Gromacs
Gunnar Widtfeldt Reginsson wrote: Hi. I am a new user of Gromacs. My question is both PyMol and Gromacs related. I tried the PyMol users mailing list but couldn't find anything. I have a small organic molecule that I am inserting into DNA in pymol. I have the DNA as one pdb file and the organic molecule as another pdb file. I open the DNA file in pymol and then load the organic molecule. After docking the organic molecule I write "save name.pdb" When viewing the name.pdb file in pymol there are some bonds between the organic molecule and the DNA that I don't want. Somehow pymol creates them and I don't see those bonds in the name.pdb file when I open it in a text reader. I then create a .gro file with pdb2gmx of the DNA.pdb and a .gro file of the organic molecule with topolbuilder 1.2 , and unite those .gro files and convert into a .pdb with editconf The newly created pdb file still has those unwanted bonds. My question is: Can I ignore those bonds? If not, how can I prevent pymol making those bonds? For the purposes of simulation, a bond is defined in the topology, not the coordinate file. What you are seeing is simply an artifact of the heuristic methods that visualization programs use to guess where bonds "should" be. -Justin Thanks. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Adsorption energy of a single molecule
Darrell Koskinen wrote: Hi Justin, So when I create the index file with the molecule and the graphene sheet and run g_energy, is the adsorption energy between the adsorbed molecule and the graphene sheet the LJ (SR) energy? And will this energy be just the interaction energy between the adsorbed molecule and the graphene sheet (i.e. does the creation of the new index file and executing -rerun cause g_energy to exclude the energies between the other molecules and the graphene sheet)? Unless you have set some special energygrp_excl in the .mdp file, then nothing should be excluded; the use of energygrps simply decomposes the energy terms into the species of interest. As for what the adsorption energy is, it may well be LJ(SR), provided there are no Coulombic terms to worry about, but I don't know anything about your parameters, so I can't say definitively. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Constraints & Restraints
Darrell Koskinen wrote: Hi Tsjerk, So then, if I understand correctly, setting "constraints = all-bonds" is not as realistic as setting "constraints = none", since the latter will allow for flexible (e.g. harmonic) behavoir which is more realistic than fixing the bond to a certain distance, correct? Actually not. It would be a better model of a harmonic potential (duh), but it has been shown that the use of constraints can lead to a (more?) acceptable model of a real system, and they allow a larger integration time to boot. Check out the papers for the constraint algorithms (refs in GROMACS manual). Mark Date: Wed, 11 Nov 2009 21:45:44 +0100 From: Tsjerk Wassenaar Subject: Re: [gmx-users] Constraints & Restraints To: Discussion list for GROMACS users Message-ID: <8ff89815091245u63c6aa65sa839f24634352...@mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Darrell, Constraints and restraints also apply to relative positions. A bond constraint fixes the bond to a certain distance. constraints = all-bonds means that all bonds are to be converted to constraints, rather than have them flexible, e.g. harmonic. Harmonic bonds are actually more like restraints, penalizing deviations from the equilibrium values. These equilibrium values and the 'penalty function' are described in the force field. Hope it helps, Tsjerk On Wed, Nov 11, 2009 at 9:32 PM, wrote: Hi, I just have a quick question on contraints and restraints. My understanding is that "constraints" fix the position of an atom in space and "restraints" restrain the deviation of the atom's position from its equilibrium point. Is that correct? If so, then I am a little confused by the purpose of "constraints = all-bonds" or "constraints = none" in an mdp file, since by selection of a force field, which has bond/angle/dihedral stretching/bending/torsion constants, we are specifying the constraints applied to the simulation. So then what is the purpose of "constraints = all-bonds" and "constraints = none"? Thanks. Darrell -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Docking with PyMol and using Gromacs
Coordinate files like pdb and gro aren't used by GROMACS to provide any bonding information. That is what the topology files are for. So their "presence" in your pdb isn't an issue. Actually, what is probably happening is that PyMol is guessing the bonds presence, based on the distance between atoms, and displaying it (which is what VMD does as well). So the bonds aren't actually there at all in the pdb file. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Gunnar Widtfeldt Reginsson Sent: Thursday, 12 November 2009 10:13 AM To: gmx-users@gromacs.org Subject: [gmx-users] Docking with PyMol and using Gromacs Hi. I am a new user of Gromacs. My question is both PyMol and Gromacs related. I tried the PyMol users mailing list but couldn't find anything. I have a small organic molecule that I am inserting into DNA in pymol. I have the DNA as one pdb file and the organic molecule as another pdb file. I open the DNA file in pymol and then load the organic molecule. After docking the organic molecule I write "save name.pdb" When viewing the name.pdb file in pymol there are some bonds between the organic molecule and the DNA that I don't want. Somehow pymol creates them and I don't see those bonds in the name.pdb file when I open it in a text reader. I then create a .gro file with pdb2gmx of the DNA.pdb and a .gro file of the organic molecule with topolbuilder 1.2 , and unite those .gro files and convert into a .pdb with editconf The newly created pdb file still has those unwanted bonds. My question is: Can I ignore those bonds? If not, how can I prevent pymol making those bonds? 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Docking with PyMol and using Gromacs
Justin A. Lemkul wrote: Gunnar Widtfeldt Reginsson wrote: Hi. I am a new user of Gromacs. My question is both PyMol and Gromacs related. I tried the PyMol users mailing list but couldn't find anything. I have a small organic molecule that I am inserting into DNA in pymol. I have the DNA as one pdb file and the organic molecule as another pdb file. I open the DNA file in pymol and then load the organic molecule. After docking the organic molecule I write "save name.pdb" When viewing the name.pdb file in pymol there are some bonds between the organic molecule and the DNA that I don't want. Somehow pymol creates them and I don't see those bonds in the name.pdb file when I open it in a text reader. I then create a .gro file with pdb2gmx of the DNA.pdb and a .gro file of the organic molecule with topolbuilder 1.2 , and unite those .gro files and convert into a .pdb with editconf The newly created pdb file still has those unwanted bonds. My question is: Can I ignore those bonds? If not, how can I prevent pymol making those bonds? For the purposes of simulation, a bond is defined in the topology, not the coordinate file. What you are seeing is simply an artifact of the heuristic methods that visualization programs use to guess where bonds "should" be. Indeed. It's a case of the visualization programs doing "what you want" for simple usage, which is less suited for more complex usage. Given the complexity of learning to use such programs, it seems few people remember the caveats in the documentation about the generation of "bonds", or stop to wonder where they come from :-) It's also no wonder that many research groups who do MD use the simulation package most familiar to the leader (from their own doctoral days?), rather than the package best suited in the abstract to the task at hand, since the former strategy makes the best use of the accumulated wisdom of the senior researchers. 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Adsorption energy of a single molecule
Darrell Koskinen wrote:
Hi Justin,
So when I create the index file with the molecule and the graphene sheet
and run g_energy, is the adsorption energy between the adsorbed molecule
and the graphene sheet the LJ (SR) energy?
Not necessarily, unless the force field was parameterized to produce
such values. First, seek to define what you mean by adsorption (free)
energy, then consider how a simulation might measure that. Then,
consider whether any force fields exist that might achieve that. Then,
test it on a case where you have experimental data.
Other procedures run a much higher risk of producing an expensive random
number generator :-)
And will this energy be just
the interaction energy between the adsorbed molecule and the graphene
sheet (i.e. does the creation of the new index file and executing -rerun
cause g_energy to exclude the energies between the other molecules and
the graphene sheet)?
Creating an energy group causes mdrun -rerun to report the fraction of
the total nonbonded energies that are due to intra- and inter-group
interactions. See manual section 3.3
Mark
Date: Sun, 01 Nov 2009 21:27:19 -0500
From: "Justin A. Lemkul"
Subject: Re: [gmx-users] Adsorption energy of a single molecule
To: Discussion list for GROMACS users
Message-ID: <4aee4387.40...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Darrell Koskinen wrote:
Hi Justin,
Since I cannot use the original .tpr file, then do I need to run
grompp with the new index file to create a "new" .tpr file,
"mdtopolnew.tpr"? I assume I then need to modify the energygrps line
within the .mdp file to include these new energy groups and then
execute "mdrun -rerun mdtraj.trr -s mdtopolnew.tpr". Is this correct?
Yes, that is the point of the -rerun function.
Does executing "mdrun -rerun mdtraj.trr -s mdtopolnew.tpr" cause a
molecular dynamics simulation to run once again? If so, then will the
exact same molecules that adsorbed on the first MD run be the same
ones that adsorb on the second MD run?
The original coordinates are used to re-calculate the energies. No
new simulation is performed.
-Justin
Thanks.
Darrell
***
***
Date: Sun, 01 Nov 2009 19:29:36 -0500
From: "Justin A. Lemkul"
Subject: Re: [gmx-users] Adsorption energy of a single molecule
To: Discussion list for GROMACS users
Message-ID: <4aee27f0.50...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Darrell Koskinen wrote:
Hi Justin,
In my simulation, I have just over 100 ammonia molecules and, of
these > molecules, 10 to 20 adsorb onto the graphene sheet. I
initially thought > that I would need to tag each one of the ammonia
molecules, since I > would not know, in advance of running the
simulation, which of these > molecules would adsorb.
Are you suggesting that, after the initial simulation run, which
uses an > index file "index.ndx" and is comprised of three
components {System, > Grph, NH3}, I run make_ndx again to assign
each adsorbed molecule to its > own index, execute "mdrun -rerun
mdtraj.trr -s mdtopol.tpr", where > mdtraj.trr and mdtopol.tpr are
the output of the initial simulation, and > then use g_energy to
analyze the energies between the groups?
Almost. You can't use the original .tpr file if you are trying to
establish new energy monitoring groups. Hence the point of making a
new .mdp file. So, re-run the old trajectory with the new .tpr file
to take advantage of the new groups.
-Justin
-- Justin A. Lemkul Ph.D.
Candidate ICTAS Doctoral Scholar 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/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
