Re: [gmx-users] Regarding pdb2gmx and mdrun
On 7/18/17 8:15 AM, S M Bargeen Turzo wrote: Hey I have been trying to convert S100A8A9(has two chains) to .gro but after energy minimization I am not getting an integer for the total charge of the system. What is the magnitude of this non-integer charge? Did you do anything funny during pdb2gmx like using -missing? -Justin Secondly when I try to do molecular dynamics simulation using these parameters: ; 0.5 ps NVT production with Langevin thermostat and GB implicit solvent INPUT ld_seed = -1 ; Use random seed # INTEGRATOR ## define = -DPOSRES integrator = sd; Langevin thermostat dt = 0.002 ; Timestep (ps) nsteps = 250 ; Simulation duration (timesteps) nstcomm = 250 ; Center of mass motion removal interval comm_mode = angular; Center of mass motion removal mode ## ENSEMBLE ### ref_t = 300 ; System temperature (K) tau_t = 2.0 ; Thermostat time constant (ps) tc_grps = system; Apply thermostat to complete system ## IMPLICIT SOLVENT ### implicit_solvent = GBSA ; Generalized Born implicit solvent gb_algorithm = HCT ; Hawkins-Cramer-Truhlar radii calculation nstgbradii = 1 rgbradii = 0.0 ; Cutoff for Born radii calculation (A) gb_epsilon_solvent = 80 gb_saltconc = 0 sa_algorithm = Ace-approximation sa_surface_tension = 2.25936 ### NONBONDED INTERACTIONS cutoff_scheme = group ; Method of managing neighbor lists pbc = no ; Periodic boundary conditions disabled coulombtype = cut-off ; Calculate coulomb interactions using cutoff rcoulomb = 0.0 ; Coulomb cutoff of infinity vdw_type = cut-off ; Calculate van der Waals interactions using cutoff rvdw = 0.0 ; Van der Waals cutoff of infinity rlist = 0.0 ; Neighbor list cutoff nstlist = 0 ; Do not update neighbor list ### OUTPUT nstlog= 50 ; Log output interval (timesteps) nstenergy = 50 ; Energy output interval (timesteps) nstcalcenergy = 50 ; Energy calculation interval (timesteps) nstxout = 50 ; Trajectory output interval (timesteps) nstvout = 50 ; Velocity outout interval (timesteps) nstfout = 50 ; Force output interval (timesteps) I get segmentation fault(11). I don't know what this means. Can you please help me out? -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Regarding pdb2gmx and mdrun
Hey I have been trying to convert S100A8A9(has two chains) to .gro but after energy minimization I am not getting an integer for the total charge of the system. Secondly when I try to do molecular dynamics simulation using these parameters: ; 0.5 ps NVT production with Langevin thermostat and GB implicit solvent INPUT ld_seed = -1 ; Use random seed # INTEGRATOR ## define = -DPOSRES integrator = sd; Langevin thermostat dt = 0.002 ; Timestep (ps) nsteps = 250 ; Simulation duration (timesteps) nstcomm = 250 ; Center of mass motion removal interval comm_mode = angular; Center of mass motion removal mode ## ENSEMBLE ### ref_t = 300 ; System temperature (K) tau_t = 2.0 ; Thermostat time constant (ps) tc_grps = system; Apply thermostat to complete system ## IMPLICIT SOLVENT ### implicit_solvent = GBSA ; Generalized Born implicit solvent gb_algorithm = HCT ; Hawkins-Cramer-Truhlar radii calculation nstgbradii = 1 rgbradii = 0.0 ; Cutoff for Born radii calculation (A) gb_epsilon_solvent = 80 gb_saltconc = 0 sa_algorithm = Ace-approximation sa_surface_tension = 2.25936 ### NONBONDED INTERACTIONS cutoff_scheme = group ; Method of managing neighbor lists pbc = no ; Periodic boundary conditions disabled coulombtype = cut-off ; Calculate coulomb interactions using cutoff rcoulomb = 0.0 ; Coulomb cutoff of infinity vdw_type = cut-off ; Calculate van der Waals interactions using cutoff rvdw = 0.0 ; Van der Waals cutoff of infinity rlist = 0.0 ; Neighbor list cutoff nstlist = 0 ; Do not update neighbor list ### OUTPUT nstlog= 50 ; Log output interval (timesteps) nstenergy = 50 ; Energy output interval (timesteps) nstcalcenergy = 50 ; Energy calculation interval (timesteps) nstxout = 50 ; Trajectory output interval (timesteps) nstvout = 50 ; Velocity outout interval (timesteps) nstfout = 50 ; Force output interval (timesteps) I get segmentation fault(11). I don't know what this means. Can you please help me out? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] regarding pdb2gmx
Thank you very much for your help Justin. I really appreciate I would like to bother you for one last time ( as of now ;). So, if I am dealing with a non-trivial molecule like CNT or some polyelectrolyte and I mainly intend to demonstrate the non-bonding interactions with some nucleic acids (say a CNT-dsDNA ) interaction, it appears to me that I dont need to care about the DNA topology even if it lacks the said parameters but I do have to care about these while updating the cnt.itp files since grompp complains about the missing parameters in the cnt.itp file. If one does not write the [ atomtypes ] and the [ pairtypes ] sections in the cnt.itp file and misses out the sigma and epsilon terms I think it underestimates the non-bonding energy terms of interaction between DNA bases and CNT atoms in the md.edr file to some extent. I will appreciate your opinion on this statement. Thanks for your time in advance Soumadwip Research Fellow IITB India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] regarding pdb2gmx
On 5/31/15 8:37 AM, soumadwip ghosh wrote: Thank you very much for your help Justin. I really appreciate I would like to bother you for one last time ( as of now ;). So, if I am dealing with a non-trivial molecule like CNT or some polyelectrolyte and I mainly intend to demonstrate the non-bonding interactions with some nucleic acids (say a CNT-dsDNA ) interaction, it appears to me that I dont need to care about the DNA topology even if it lacks the said parameters but I do have to care about these while updating the cnt.itp files since grompp complains about the missing parameters in the cnt.itp file. If one does not write the [ atomtypes ] and the [ pairtypes ] sections in the cnt.itp file and misses out the sigma and epsilon terms I think it underestimates the non-bonding energy terms of interaction between DNA bases and CNT atoms in the md.edr file to some extent. I will appreciate your opinion on this statement. That doesn't make sense. If you are missing parameters, grompp will complain and fail with a fatal error. If grompp happily carries on and produces your .tpr, then you're getting the interactions the force field dictates because grompp found everything the molecules need in ffbonded.itp, ffnonbonded.itp, or specified in a molecule .itp. If you override grompp's messages with -maxwarn, well then that's your fault :) Also note that [pairtypes] are intramolecular terms. They do not affect DNA-CNT interactions. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] regarding pdb2gmx
Hi all,
I have a general query about the basic functioning of pdb2gmx. I
recently observed that when I take a PDB file for a DNA molecule and build
its topology via pdb2gmx (in CHARMM27 ff) it automatically builds it
without any hitches. If I look at the .itp file made for the DNA chain it
looks like,
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB
chargeB massB
; residue 1 DC rtp DC q -0.5
1ON5 1 DCO5' 1 -0.6615.9994 ;
qtot -0.66
2HN5 1 DCH5T 2 0.43 1.008 ;
qtot -0.23
3 CN8B 1 DCC5' 3 0.05 12.011 ;
qtot -0.18
4HN8 1 DC H5'1 4 0.09 1.008 ;
qtot -0.09
5HN8 1 DC H5'2 5 0.09 1.008 ;
qtot 0
6CN7 1 DCC4' 6 0.16 12.011 ;
qtot 0.16
7HN7 1 DCH4' 7 0.09 1.008 ;
qtot 0.25
8ON6 1 DCO4' 8 -0.515.9994 ;
qtot -0.25
9 CN7B 1 DCC1' 9 0.16 12.011 ;
qtot -0.09
10HN7 1 DCH1' 10 0.09 1.008 ;
qtot 0
11NN2 1 DC N1 11 -0.13 14.007 ;
qtot -0.13
12CN3 1 DC C6 12 0.05 12.011 ;
qtot -0.08
13HN3 1 DC H6 13 0.17 1.008 ;
qtot 0.09
14CN3 1 DC C5 14 -0.13 12.011 ;
qtot -0.04
15HN3 1 DC H5 15 0.07 1.008 ;
qtot 0.03
16CN1 1 DC C2 16 0.52 12.011 ;
qtot 0.55
17 ON1C 1 DC O2 17 -0.4915.9994 ;
qtot 0.06
18NN3 1 DC N3 18 -0.66 14.007 ;
qtot -0.6
19CN2 1 DC C4 19 0.65 12.011 ;
qtot 0.05
20NN1 1 DC N4 20 -0.75 14.007 ;
qtot -0.7
21HN1 1 DCH41 21 0.37 1.008 ;
qtot -0.33
22HN1 1 DCH42 22 0.33 1.008 ;
qtot 0
23CN8 1 DCC2' 23 -0.18 12.011 ;
qtot -0.18
24HN8 1 DC H2'1 24 0.09 1.008 ;
qtot -0.09
25HN8 1 DC H2'2 25 0.09 1.008 ;
qtot 0
26CN7 1 DCC3' 26 0.01 12.011 ;
qtot 0.01
27HN7 1 DCH3' 27 0.09 1.008 ;
qtot 0.1
28ON2 1 DCO3' 28 -0.5715.9994 ;
qtot -0.47
For one residue.
However, if you look at the [ bond ] section of this .itp file it looks
like,
[ bonds ]
; aiaj functc0c1c2c3
1 2 1
1 3 1
3 4 1
3 5 1
3 6 1
6 7 1
6 8 1
626 1
8 9 1
910 1
911 1
923 1
1112 1
1116 1
1213 1
There are no parameters in the right and by principle grompp should
complain about this. But the simulation runs fine and the proper
interactions with the desired outcomes are always obtained. However, things
get altered when I proceed to model anything else than a DNA/protein. As
for example, I have made a topology for tetramethyl ammonium ion ( in
CHARMM 27) and as usual it lacks these parameters in all the [ bonds ],
{angle ] or [ dihedral ] sections. I changed the .top extension to tma.itp
and included in the system topology for a double stranded DNA molecule
according to standard protocols. Now when I start grompp it screams about
the 'missing parameters in the tma.itp ffile'. My question is everytime I
model something my CHARMM, do I have to include parameters such as force
constant, phi0, b0, mult etc from the ffbonded.itp file manually or does
pdb2gmx should write it looking at the connectivity mentioned in the PDB
file? The same thing goes for writing sigma and epsilon terms from the
ffnonbonde.itp file manually or pdb2gmx should do it by default? I have
another question that is it ok not to specify the [ atomtypes ] and [
pairtypes ] in the .itp file because without these being specified
properly, is it possible that the correct non bonding interaction arises? I
have always seen SWISSPARAM and ATB topologies come with all these things
mentioned from the scratch but with pdb2gmx I have never seen it. So, is it
like pdb2gmx gives only the atoms making the bonds, angles, prop and
improp. dihedrals (atomtypes already mentioned in the aminoacids.rtp file)
and the rest of the parameters are to placed manually or am i missing
something regarding pdb2gmx( some flags)??
Recently, I wanted to simulate graphene and although the ideal job is to go
with g_x2top, issuing
Re: [gmx-users] regarding pdb2gmx
On 5/30/15 6:40 AM, soumadwip ghosh wrote:
Hi all,
I have a general query about the basic functioning of pdb2gmx. I
recently observed that when I take a PDB file for a DNA molecule and build
its topology via pdb2gmx (in CHARMM27 ff) it automatically builds it
without any hitches. If I look at the .itp file made for the DNA chain it
looks like,
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB
chargeB massB
; residue 1 DC rtp DC q -0.5
1ON5 1 DCO5' 1 -0.6615.9994 ;
qtot -0.66
2HN5 1 DCH5T 2 0.43 1.008 ;
qtot -0.23
3 CN8B 1 DCC5' 3 0.05 12.011 ;
qtot -0.18
4HN8 1 DC H5'1 4 0.09 1.008 ;
qtot -0.09
5HN8 1 DC H5'2 5 0.09 1.008 ;
qtot 0
6CN7 1 DCC4' 6 0.16 12.011 ;
qtot 0.16
7HN7 1 DCH4' 7 0.09 1.008 ;
qtot 0.25
8ON6 1 DCO4' 8 -0.515.9994 ;
qtot -0.25
9 CN7B 1 DCC1' 9 0.16 12.011 ;
qtot -0.09
10HN7 1 DCH1' 10 0.09 1.008 ;
qtot 0
11NN2 1 DC N1 11 -0.13 14.007 ;
qtot -0.13
12CN3 1 DC C6 12 0.05 12.011 ;
qtot -0.08
13HN3 1 DC H6 13 0.17 1.008 ;
qtot 0.09
14CN3 1 DC C5 14 -0.13 12.011 ;
qtot -0.04
15HN3 1 DC H5 15 0.07 1.008 ;
qtot 0.03
16CN1 1 DC C2 16 0.52 12.011 ;
qtot 0.55
17 ON1C 1 DC O2 17 -0.4915.9994 ;
qtot 0.06
18NN3 1 DC N3 18 -0.66 14.007 ;
qtot -0.6
19CN2 1 DC C4 19 0.65 12.011 ;
qtot 0.05
20NN1 1 DC N4 20 -0.75 14.007 ;
qtot -0.7
21HN1 1 DCH41 21 0.37 1.008 ;
qtot -0.33
22HN1 1 DCH42 22 0.33 1.008 ;
qtot 0
23CN8 1 DCC2' 23 -0.18 12.011 ;
qtot -0.18
24HN8 1 DC H2'1 24 0.09 1.008 ;
qtot -0.09
25HN8 1 DC H2'2 25 0.09 1.008 ;
qtot 0
26CN7 1 DCC3' 26 0.01 12.011 ;
qtot 0.01
27HN7 1 DCH3' 27 0.09 1.008 ;
qtot 0.1
28ON2 1 DCO3' 28 -0.5715.9994 ;
qtot -0.47
For one residue.
However, if you look at the [ bond ] section of this .itp file it looks
like,
[ bonds ]
; aiaj functc0c1c2c3
1 2 1
1 3 1
3 4 1
3 5 1
3 6 1
6 7 1
6 8 1
626 1
8 9 1
910 1
911 1
923 1
1112 1
1116 1
1213 1
There are no parameters in the right and by principle grompp should
complain about this. But the simulation runs fine and the proper
interactions with the desired outcomes are always obtained. However, things
get altered when I proceed to model anything else than a DNA/protein. As
for example, I have made a topology for tetramethyl ammonium ion ( in
CHARMM 27) and as usual it lacks these parameters in all the [ bonds ],
{angle ] or [ dihedral ] sections. I changed the .top extension to tma.itp
and included in the system topology for a double stranded DNA molecule
according to standard protocols. Now when I start grompp it screams about
the 'missing parameters in the tma.itp ffile'. My question is everytime I
model something my CHARMM, do I have to include parameters such as force
constant, phi0, b0, mult etc from the ffbonded.itp file manually or does
pdb2gmx should write it looking at the connectivity mentioned in the PDB
file? The same thing goes for writing sigma and epsilon terms from the
ffnonbonde.itp file manually or pdb2gmx should do it by default? I have
another question that is it ok not to specify the [ atomtypes ] and [
pairtypes ] in the .itp file because without these being specified
properly, is it possible that the correct non bonding interaction arises? I
have always seen SWISSPARAM and ATB topologies come with all these things
mentioned from the scratch but with pdb2gmx I have never seen it. So, is it
like pdb2gmx gives only the atoms making the bonds, angles, prop and
improp. dihedrals (atomtypes already mentioned in the aminoacids.rtp file)
and the rest of the parameters are to placed manually or am i missing
something regarding pdb2gmx( some flags)??
Re: [gmx-users] regarding pdb2gmx
Thanks Justin for your insights. So when I am making the topology of DNA via ppdb2gmx using CHARMM, the parameters in the .itp files are not adequate and I should place them manually everytime I make a molecule topology with pdb2gmx? In some of my previous works actually the DNA molecule gave outcomes which were pretty much expected. So, just like I have put all the missing parameters in the .cnt.itp file should I do the same with the dna.itp generated by pdb2gmx in order to ensure correct interactions? thanks for your time in advance Soumadwip Research Fellow IITB India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] regarding pdb2gmx
On 5/30/15 10:24 AM, soumadwip ghosh wrote: Thanks Justin for your insights. So when I am making the topology of DNA via ppdb2gmx using CHARMM, the parameters in the .itp files are not adequate and I should place them manually everytime I make a molecule topology with pdb2gmx? In some of my previous works actually the DNA molecule gave outcomes which were pretty much expected. So, just like I have put all the missing parameters in the .cnt.itp file should I do the same with the dna.itp generated by pdb2gmx in order to ensure correct interactions? No. The parameters for DNA exist in the force field, so grompp looks them up, finds them, and carries on happily. Again, this is how all the force fields work except GROMOS. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
