Re: [gmx-users] How to automate genion completely?
On 25/03/2012 12:43 PM, John Ladasky wrote:
I am starting to write my own turnkey scripts to automate GROMACS (v
4.5.4) work flow. Many of the GROMACS commands, such as pdb2gmx and
genion, have interactive options by default, meaning that you manually
enter information when the program runs.
In the tutorials, we are taught to invoke pdb2gmx from the command
line using certain arguments which name input and output files. But
then, we choose our force field from a numbered menu inside pdb2gmx.
However, if you know the name of the force field (these names SHOULD
be listed somewhere!),
Sure, you can find them the same place pdb2gmx does - as ${name}.ff
directories in working directory or under $GMXLIB.
you can use the -ff argument when you call pdb2gmx from the shell.
For example, -ff gromos45a3. Then you do not have to manually enter
anything.
I am looking for a corresponding option for genion. Genion offers a
numbered menu to ask you which group of atoms you wish to use for ion
replacements. The groups that most of us would want to use are the
Water or SOL groups. With the files that I'm working with right
now, these pop up as groups #12 and #13, respectively. But they
needn't always be numbered this way, if the user has altered the
standard .ndx file.
Is there an argument that one can supply to genion from the command
prompt which will select the replacement group automatically, as -ff
selects a force field for pdb2gmx? I have the v. 4.5.4 manual. I do
not see the argument (pp. 273-4). I hope that it exists, and that it
is just undocumented.
That does seem to be a gap in the manual. I've expanded the discussion
in section 8.1 of the manual to include:
+Each tool that can use groups will offer the available alternatives
+for the user to choose. That choice can be made with the number of the
+group, or its name. In fact, the first few letters of the group
+name will suffice if that will distinguish the group from all others.
+There are ways to use Unix shell features to choose group names
+on the command line, rather than interactively. Consult the GROMACS
+webpage for suggestions.
+
Mark
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[gmx-users] Adjust time intervals
Dear users, When I got total energy.xvg file for plotting total energy via time, data haven't saved in order time intervals. What command can control time intervals in .mdp for .edr file? To better understand I pasted some text from total energy.xvg file. As you see, time intervals aren't same. @ s0 legend Total Energy 0.00 -274454.75 12.420001 -274884.187500 18.060001 -274532.343750 20.00 -274475.437500 29.360001 -275739.562500 35.00 -274441.937500 40.00 -274463.156250 46.280003 -273342.25 51.920002 -273099.718750 57.580002 -274429.25 60.04 -274844.062500 68.860001 -273905.093750 74.50 -273988.812500 80.00 -276057.625000 Thanks very much in advance Afsaneh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Adjust time intervals
In the .mdp file what is nstenergy set to? On 2012-03-25 04:37:59PM +0430, afsaneh maleki wrote: Dear users, When I got total energy.xvg file for plotting total energy via time, data haven't saved in order time intervals. What command can control time intervals in .mdp for .edr file? To better understand I pasted some text from total energy.xvg file. As you see, time intervals aren't same. @ s0 legend Total Energy 0.00 -274454.75 12.420001 -274884.187500 18.060001 -274532.343750 20.00 -274475.437500 29.360001 -275739.562500 35.00 -274441.937500 40.00 -274463.156250 46.280003 -273342.25 51.920002 -273099.718750 57.580002 -274429.25 60.04 -274844.062500 68.860001 -273905.093750 74.50 -273988.812500 80.00 -276057.625000 Thanks very much in advance Afsaneh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Adjust time intervals
Peter C. Lai wrote: In the .mdp file what is nstenergy set to? I'd further ask what the rest of the .mdp file says, as well. If this is the output of energy minimization, it's totally normal. The output seems irregular but is due (I believe) to the potentially uneven step size taken during EM. -Justin On 2012-03-25 04:37:59PM +0430, afsaneh maleki wrote: Dear users, When I got total energy.xvg file for plotting total energy via time, data haven't saved in order time intervals. What command can control time intervals in .mdp for .edr file? To better understand I pasted some text from total energy.xvg file. As you see, time intervals aren't same. @ s0 legend Total Energy 0.00 -274454.75 12.420001 -274884.187500 18.060001 -274532.343750 20.00 -274475.437500 29.360001 -275739.562500 35.00 -274441.937500 40.00 -274463.156250 46.280003 -273342.25 51.920002 -273099.718750 57.580002 -274429.25 60.04 -274844.062500 68.860001 -273905.093750 74.50 -273988.812500 80.00 -276057.625000 Thanks very much in advance Afsaneh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Adjust time intervals
Thanks Dear Peter and Justin for reply, I paste some text from .mdp for calculation of free energy. I have done calculation of minimization energy before. title = production for ile-pro-SOL ; Run parameters integrator= sd ; leap-frog integrator nsteps= 100 ; 0.002* 100 = 2000 ps (2 ns) dt = 0.002 ; 2 fs tinit =0 ; Output control nstxout = 10; save coordinates every 0.2 ps nstvout =10 ; save velocities every 0.2 ps nstxtcout =10 ; xtc compressed trajectory output every 2 ps nstenergy = 1 ; save energies every 0.2 ps nstlog = 1 ; update log file every 0.2 ps xtc_precision =1000 ; Bond parameters constraint_algorithm = lincs ; holonomic constraints constraints= all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 2 ; accuracy of LINCS unconstrained_start=no lincs_order=12 lincs_warnangle=30 shake-tol =0.0001 ; Neighborsearching ns_type = grid; search neighboring grid cels nstlist = 10 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r= 1.2 ; Method for doing Van der Waals = vdw-type = switch ; cut-off lengths= rvdw-switch = 1. rvdw =1.1 ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics ; EWALD/PME/PPPM parameters = pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on ;tcoupl = Nose-Hoover ; More accurate thermostat ;pcoupl =Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic tau_p= 5.0 ; time constant, in ps ref_p= 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-5 ; isothermal compressibility, bar^-1 ;restraints ;dihre=simple dihre-fc=1 nstdihreout=1000 disre=simple disre_fc=1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme Thanks, Afsaneh On 3/25/12, Justin A. Lemkul jalem...@vt.edu wrote: Peter C. Lai wrote: In the .mdp file what is nstenergy set to? I'd further ask what the rest of the .mdp file says, as well. If this is the output of energy minimization, it's totally normal. The output seems irregular but is due (I believe) to the potentially uneven step size taken during EM. -Justin On 2012-03-25 04:37:59PM +0430, afsaneh maleki wrote: Dear users, When I got total energy.xvg file for plotting total energy via time, data haven't saved in order time intervals. What command can control time intervals in .mdp for .edr file? To better understand I pasted some text from total energy.xvg file. As you see, time intervals aren't same. @ s0 legend Total Energy 0.00 -274454.75 12.420001 -274884.187500 18.060001 -274532.343750 20.00 -274475.437500 29.360001 -275739.562500 35.00 -274441.937500 40.00 -274463.156250 46.280003 -273342.25 51.920002 -273099.718750 57.580002 -274429.25 60.04 -274844.062500 68.860001 -273905.093750 74.50 -273988.812500 80.00 -276057.625000 Thanks very much in advance Afsaneh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post
Re: [gmx-users] Adjust time intervals
afsaneh maleki wrote: Thanks Dear Peter and Justin for reply, I paste some text from .mdp for calculation of free energy. I have done calculation of minimization energy before. Which Gromacs version are you using? I can't reproduce your problem with version 4.5.4 or 4.5.5, either with or without the free energy code. My energy outputs are always present at the nstenergy interval. -Justin title = production for ile-pro-SOL ; Run parameters integrator= sd ; leap-frog integrator nsteps= 100 ; 0.002* 100 = 2000 ps (2 ns) dt = 0.002 ; 2 fs tinit =0 ; Output control nstxout = 10; save coordinates every 0.2 ps nstvout =10 ; save velocities every 0.2 ps nstxtcout =10 ; xtc compressed trajectory output every 2 ps nstenergy = 1 ; save energies every 0.2 ps nstlog = 1 ; update log file every 0.2 ps xtc_precision =1000 ; Bond parameters constraint_algorithm = lincs ; holonomic constraints constraints= all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 2 ; accuracy of LINCS unconstrained_start=no lincs_order=12 lincs_warnangle=30 shake-tol =0.0001 ; Neighborsearching ns_type = grid; search neighboring grid cels nstlist = 10 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r= 1.2 ; Method for doing Van der Waals = vdw-type = switch ; cut-off lengths= rvdw-switch = 1. rvdw =1.1 ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics ; EWALD/PME/PPPM parameters = pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on ;tcoupl = Nose-Hoover ; More accurate thermostat ;pcoupl =Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic tau_p= 5.0 ; time constant, in ps ref_p= 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-5 ; isothermal compressibility, bar^-1 ;restraints ;dihre=simple dihre-fc=1 nstdihreout=1000 disre=simple disre_fc=1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme Thanks, Afsaneh On 3/25/12, Justin A. Lemkul jalem...@vt.edu wrote: Peter C. Lai wrote: In the .mdp file what is nstenergy set to? I'd further ask what the rest of the .mdp file says, as well. If this is the output of energy minimization, it's totally normal. The output seems irregular but is due (I believe) to the potentially uneven step size taken during EM. -Justin On 2012-03-25 04:37:59PM +0430, afsaneh maleki wrote: Dear users, When I got total energy.xvg file for plotting total energy via time, data haven't saved in order time intervals. What command can control time intervals in .mdp for .edr file? To better understand I pasted some text from total energy.xvg file. As you see, time intervals aren't same. @ s0 legend Total Energy 0.00 -274454.75 12.420001 -274884.187500 18.060001 -274532.343750 20.00 -274475.437500 29.360001 -275739.562500 35.00 -274441.937500 40.00 -274463.156250 46.280003 -273342.25 51.920002 -273099.718750 57.580002 -274429.25 60.04 -274844.062500 68.860001 -273905.093750 74.50 -273988.812500 80.00 -276057.625000 Thanks very much in advance Afsaneh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing
Re: [gmx-users] Adjust time intervals
Dear Justin, I use version 4.0.7 Thanks Afsaneh On 3/25/12, Justin A. Lemkul jalem...@vt.edu wrote: afsaneh maleki wrote: Thanks Dear Peter and Justin for reply, I paste some text from .mdp for calculation of free energy. I have done calculation of minimization energy before. Which Gromacs version are you using? I can't reproduce your problem with version 4.5.4 or 4.5.5, either with or without the free energy code. My energy outputs are always present at the nstenergy interval. -Justin title= production for ile-pro-SOL ; Run parameters integrator = sd ; leap-frog integrator nsteps = 100 ; 0.002* 100 = 2000 ps (2 ns) dt = 0.002 ; 2 fs tinit =0 ; Output control nstxout = 10; save coordinates every 0.2 ps nstvout =10 ; save velocities every 0.2 ps nstxtcout =10 ; xtc compressed trajectory output every 2 ps nstenergy= 1 ; save energies every 0.2 ps nstlog = 1 ; update log file every 0.2 ps xtc_precision =1000 ; Bond parameters constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 2 ; accuracy of LINCS unconstrained_start=no lincs_order=12 lincs_warnangle=30 shake-tol =0.0001 ; Neighborsearching ns_type= grid; search neighboring grid cels nstlist= 10 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r= 1.2 ; Method for doing Van der Waals = vdw-type = switch ; cut-off lengths= rvdw-switch = 1. rvdw =1.1 ; Electrostatics coulombtype= PME ; Particle Mesh Ewald for long-range electrostatics ; EWALD/PME/PPPM parameters = pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on ;tcoupl= Nose-Hoover ; More accurate thermostat ;pcoupl=Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype= isotropic tau_p = 5.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-5; isothermal compressibility, bar^-1 ;restraints ;dihre=simple dihre-fc=1 nstdihreout=1000 disre=simple disre_fc=1 ; Periodic boundary conditions pbc= xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme Thanks, Afsaneh On 3/25/12, Justin A. Lemkul jalem...@vt.edu wrote: Peter C. Lai wrote: In the .mdp file what is nstenergy set to? I'd further ask what the rest of the .mdp file says, as well. If this is the output of energy minimization, it's totally normal. The output seems irregular but is due (I believe) to the potentially uneven step size taken during EM. -Justin On 2012-03-25 04:37:59PM +0430, afsaneh maleki wrote: Dear users, When I got total energy.xvg file for plotting total energy via time, data haven't saved in order time intervals. What command can control time intervals in .mdp for .edr file? To better understand I pasted some text from total energy.xvg file. As you see, time intervals aren't same. @ s0 legend Total Energy 0.00 -274454.75 12.420001 -274884.187500 18.060001 -274532.343750 20.00 -274475.437500 29.360001 -275739.562500 35.00 -274441.937500 40.00 -274463.156250 46.280003 -273342.25 51.920002 -273099.718750 57.580002 -274429.25 60.04 -274844.062500 68.860001 -273905.093750 74.50 -273988.812500 80.00 -276057.625000 Thanks very much in advance Afsaneh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D.
Re: [gmx-users] Adjust time intervals
afsaneh maleki wrote: Dear Justin, I use version 4.0.7 I don't recall any specific bug related to this problem, but when using outdated software (several years old in this case), the first step is to upgrade to the newest version and try again. Development in the 4.0.x series is no longer ongoing, so fixing any potential bugs there is not likely to happen. If the problem is reproducible in the newest version, it will need to be investigated further. -Justin Thanks Afsaneh On 3/25/12, Justin A. Lemkul jalem...@vt.edu wrote: afsaneh maleki wrote: Thanks Dear Peter and Justin for reply, I paste some text from .mdp for calculation of free energy. I have done calculation of minimization energy before. Which Gromacs version are you using? I can't reproduce your problem with version 4.5.4 or 4.5.5, either with or without the free energy code. My energy outputs are always present at the nstenergy interval. -Justin title = production for ile-pro-SOL ; Run parameters integrator= sd ; leap-frog integrator nsteps= 100 ; 0.002* 100 = 2000 ps (2 ns) dt = 0.002 ; 2 fs tinit =0 ; Output control nstxout = 10; save coordinates every 0.2 ps nstvout =10 ; save velocities every 0.2 ps nstxtcout =10 ; xtc compressed trajectory output every 2 ps nstenergy = 1 ; save energies every 0.2 ps nstlog = 1 ; update log file every 0.2 ps xtc_precision =1000 ; Bond parameters constraint_algorithm = lincs ; holonomic constraints constraints= all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 2 ; accuracy of LINCS unconstrained_start=no lincs_order=12 lincs_warnangle=30 shake-tol =0.0001 ; Neighborsearching ns_type = grid; search neighboring grid cels nstlist = 10 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r= 1.2 ; Method for doing Van der Waals = vdw-type = switch ; cut-off lengths= rvdw-switch = 1. rvdw =1.1 ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics ; EWALD/PME/PPPM parameters = pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on ;tcoupl = Nose-Hoover ; More accurate thermostat ;pcoupl =Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic tau_p= 5.0 ; time constant, in ps ref_p= 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-5 ; isothermal compressibility, bar^-1 ;restraints ;dihre=simple dihre-fc=1 nstdihreout=1000 disre=simple disre_fc=1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme Thanks, Afsaneh On 3/25/12, Justin A. Lemkul jalem...@vt.edu wrote: Peter C. Lai wrote: In the .mdp file what is nstenergy set to? I'd further ask what the rest of the .mdp file says, as well. If this is the output of energy minimization, it's totally normal. The output seems irregular but is due (I believe) to the potentially uneven step size taken during EM. -Justin On 2012-03-25 04:37:59PM +0430, afsaneh maleki wrote: Dear users, When I got total energy.xvg file for plotting total energy via time, data haven't saved in order time intervals. What command can control time intervals in .mdp for .edr file? To better understand I pasted some text from total energy.xvg file. As you see, time intervals aren't same. @ s0 legend Total Energy 0.00 -274454.75 12.420001 -274884.187500 18.060001 -274532.343750 20.00 -274475.437500 29.360001 -275739.562500 35.00 -274441.937500 40.00 -274463.156250 46.280003 -273342.25 51.920002 -273099.718750 57.580002 -274429.25 60.04 -274844.062500 68.860001 -273905.093750 74.50 -273988.812500 80.00 -276057.625000 Thanks very much in advance Afsaneh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at
Re: [gmx-users] Fatal error: Atom CG is used in the topology database...
Any suggestions for programmatically repairing the pdb, i.e. Guessing the missing residue atoms and adding them at the appropriate coordinates? I tried vmd's autopsf, which works, but evidently vmd's implementation of charm27 is different than Gromac's, it adds atom types not present in Gromac's charm27. I looked into whatif, but unfortunately it's not free OSS. Wonder if I could use vmd's autopsf, and then write something that changes the atom types?? Any ideas? Thanks On Mar 23, 2012, at 5:39 PM, Justin A. Lemkul jalem...@vt.edu wrote: Andy Somogyi wrote: Hi All, I'm trying to generate topology for a PDB from viperdb, PDB ID 1DZL, http://viperdb.scripps.edu/info_page.php?VDB=1dzl using pdb2gmx -f 1dzl_full.pdb -o test.pdb -p test.top I've tried CHARMM27 and AMBER03 FFs, water none and I get the result: Fatal error: Atom CG is used in the topology database, but an atom of that name was not found in residue number 1. I have not have much luck finding this error in any mailing list. I've never seen that error before, but it sounds like there is an atom named 'CG' in the .rtp entry but not in the coordinate file. Either the atom is named differently or it is missing. If the PDB does have missing atoms, can pdb2gmx guess missing atoms like VMD's psf gen? No. The contents of the input coordinate file must match what is expected by the .rtp file. If you have missing atoms, they must be modeled in using external software. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Fatal error: Atom CG is used in the topology database...
Andy Somogyi wrote: Any suggestions for programmatically repairing the pdb, i.e. Guessing the missing residue atoms and adding them at the appropriate coordinates? I tried vmd's autopsf, which works, but evidently vmd's implementation of charm27 is different than Gromac's, it adds atom types not present in Gromac's charm27. I looked into whatif, but unfortunately it's not free OSS. Wonder if I could use vmd's autopsf, and then write something that changes the atom types?? Any ideas? My favorite tool for simple sidechain rebuilding: http://spdbv.vital-it.ch/ It offers a rotamer library and the naming conforms to the normal standard so there are no issues when using the fixed files as input into pdb2gmx. -Justin Thanks On Mar 23, 2012, at 5:39 PM, Justin A. Lemkul jalem...@vt.edu wrote: Andy Somogyi wrote: Hi All, I'm trying to generate topology for a PDB from viperdb, PDB ID 1DZL, http://viperdb.scripps.edu/info_page.php?VDB=1dzl using pdb2gmx -f 1dzl_full.pdb -o test.pdb -p test.top I've tried CHARMM27 and AMBER03 FFs, water none and I get the result: Fatal error: Atom CG is used in the topology database, but an atom of that name was not found in residue number 1. I have not have much luck finding this error in any mailing list. I've never seen that error before, but it sounds like there is an atom named 'CG' in the .rtp entry but not in the coordinate file. Either the atom is named differently or it is missing. If the PDB does have missing atoms, can pdb2gmx guess missing atoms like VMD's psf gen? No. The contents of the input coordinate file must match what is expected by the .rtp file. If you have missing atoms, they must be modeled in using external software. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Dimethyl Sulfoxide EM Absorbance
Hi All, I would greatly appreciate it if anyone could provide a reference or information on the electromagnetic absorbance characteristics of dimethyl sulfoxide, especially in the region of 800-1400nm. Thank you, Nancy -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] grompp is adding a bond in my model that should not be there
I made a model of a receptor protein, bilayer, and solvent. My protein contains a 20 residue gap. This gap corresponds to a region of the protein that had been digested by trypsin before crystallization. The trypsin digestion has no affect on receptor activity experimentally. I performed energy minimization without problem. The protein looked like it should, containing the gap. When I performed equilibration, the output had the C-terminus of one protein fragment connected to the N-terminus of the other protein fragment. I don't know how this peptide bond was created, because it was not in the input *.gro file to grompp. Please help. Jackson Chief Elk Graduate Student in Biophysics and Biochemistry The University of Montana Missoula, MT -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] error in oscillation period
Hello everyone, I am getting the following error when i execute grompp command ,can anyone please explain me why this error arises, *NOTE 2 [file ile.top, line 2986]: The bond in molecule-type Protein_chain_I between atoms 22 N and 23 HN has an estimated oscillational period of 1.0e-02 ps, which is less than 10 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. *Thank you in advance, --Mohan gmx-users@gromacs.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] grompp is adding a bond in my model that should not be there
On 26/03/2012 12:20 PM, Jackson Chief wrote: I made a model of a receptor protein, bilayer, and solvent. My protein contains a 20 residue gap. This gap corresponds to a region of the protein that had been digested by trypsin before crystallization. The trypsin digestion has no affect on receptor activity experimentally. I performed energy minimization without problem. The protein looked like it should, containing the gap. You have to treat this gap somehow. Either you have to cap the peptide chains (see pdb2gmx -h), or model in the missing residues using some (non-GROMACS) software. When I performed equilibration, the output had the C-terminus of one protein fragment connected to the N-terminus of the other protein fragment. I don't know how this peptide bond was created, because it was not in the input *.gro file to grompp. Please help. .gro files have coordinates, never bonds. Since you haven't described how you are treating the gap, and haven't said how you've observed the creation of a peptide bond, it's hard to give specific guidance. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error in oscillation period
On 26/03/2012 2:02 PM, mohan maruthi sena wrote: Hello everyone, I am getting the following error when i execute grompp command ,can anyone please explain me why this error arises, *NOTE 2 [file ile.top, line 2986]: The bond in molecule-type Protein_chain_I between atoms 22 N and 23 HN has an estimated oscillational period of 1.0e-02 ps, which is less than 10 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. * It's self-explanatory if you understand the ideas in 6.5 of the manual. In the absence of information about your .mdp file and the indicated bond distance, there's nothing else to be said. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] grompp is adding a bond in my model that should not be there
The missing residues correspond to a loop that connects two alpha helices. The C-terminal end of one helix, and N-terminal end of the other helix contain a random coil. After energy minimization, the coils are extended in space and not connected. I visualized this by looking at the .gro file in VMD. After 5ns of unrestrained MD, the two coils are clearly connected by looking at the output .gro file in VMD. Weird. On Sun, Mar 25, 2012 at 9:48 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 26/03/2012 12:20 PM, Jackson Chief wrote: I made a model of a receptor protein, bilayer, and solvent. My protein contains a 20 residue gap. This gap corresponds to a region of the protein that had been digested by trypsin before crystallization. The trypsin digestion has no affect on receptor activity experimentally. I performed energy minimization without problem. The protein looked like it should, containing the gap. You have to treat this gap somehow. Either you have to cap the peptide chains (see pdb2gmx -h), or model in the missing residues using some (non-GROMACS) software. When I performed equilibration, the output had the C-terminus of one protein fragment connected to the N-terminus of the other protein fragment. I don't know how this peptide bond was created, because it was not in the input *.gro file to grompp. Please help. .gro files have coordinates, never bonds. Since you haven't described how you are treating the gap, and haven't said how you've observed the creation of a peptide bond, it's hard to give specific guidance. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] grompp is adding a bond in my model that should not be there
Hey, The problem is likely that pdb2gmx created the bond. It will have given a long bond warning. You can add a ter statement in the pdb file at the break. Cheers, Tsjerk On Mar 26, 2012 5:49 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 26/03/2012 12:20 PM, Jackson Chief wrote: I made a model of a receptor protein, bilayer, and ... You have to treat this gap somehow. Either you have to cap the peptide chains (see pdb2gmx -h), or model in the missing residues using some (non-GROMACS) software. When I performed equilibration, the output had the C-terminus of one protein fragment connecte... .gro files have coordinates, never bonds. Since you haven't described how you are treating the gap, and haven't said how you've observed the creation of a peptide bond, it's hard to give specific guidance. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
