Re: [gmx-users] Potential issue using acpype to convert amber topology to gromacs
Hi Justin, That makes sense, I've found where the parameters are Thanks for your help James From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul <jalem...@vt.edu> Sent: 14 February 2018 22:31:07 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Potential issue using acpype to convert amber topology to gromacs On 2/14/18 5:28 PM, Easton J.W. wrote: > Hi Justin, > > Many thanks for the detailed reply. > > I just wanted to check that it doesn't matter that the A2C and A3C are not > present in the bonded and non-bonded itp files for the forcefield? Should > this not have given an error? The topology snippet you showed an [atomtypes] directive with those types defined, so they were in fact in the nonbonded parameter list by virtue of being added just above the first [moleculetype], as is permitted in GROMACS topologies. If there were missing parameters, grompp would have failed with a fatal error, so presumably you also included the necessary bonded parameters somewhere, too. -Justin > Kind regards, > > James > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin > Lemkul <jalem...@vt.edu> > Sent: 14 February 2018 14:43:35 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Potential issue using acpype to convert amber > topology to gromacs > > > > On 2/14/18 9:42 AM, Justin Lemkul wrote: >> >> On 2/14/18 9:33 AM, Easton J.W. wrote: >>> Thanks Justin, >>> >>> >>> Will this effect the interactions (both bonded and non-bonded) that >>> these atoms have, as their atom types are not in the forcefield itp >>> files? >> Missing atom types would cause grompp to fail; you'd never get to the >> point where a simulation would be affected. >> >> You're introducing custom atom types in the topology itself, and >> that's always legal before any [moleculetype] appears. The LJ >> parameters come from the [atomtypes] directive. Masses and charges >> present in that directive aren't used. >> > Actually, to clarify: *if* masses are present in the [atoms] directive > of a [moleculetype], then the masses found in [atomtypes] are not used. > Strictly speaking, it is not necessary to have explicit masses in > [atoms], though nearly all topologies do. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > == > > -- > 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. -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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. -- 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] Potential issue using acpype to convert amber topology to gromacs
On 2/14/18 5:28 PM, Easton J.W. wrote: Hi Justin, Many thanks for the detailed reply. I just wanted to check that it doesn't matter that the A2C and A3C are not present in the bonded and non-bonded itp files for the forcefield? Should this not have given an error? The topology snippet you showed an [atomtypes] directive with those types defined, so they were in fact in the nonbonded parameter list by virtue of being added just above the first [moleculetype], as is permitted in GROMACS topologies. If there were missing parameters, grompp would have failed with a fatal error, so presumably you also included the necessary bonded parameters somewhere, too. -Justin Kind regards, James From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul <jalem...@vt.edu> Sent: 14 February 2018 14:43:35 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Potential issue using acpype to convert amber topology to gromacs On 2/14/18 9:42 AM, Justin Lemkul wrote: On 2/14/18 9:33 AM, Easton J.W. wrote: Thanks Justin, Will this effect the interactions (both bonded and non-bonded) that these atoms have, as their atom types are not in the forcefield itp files? Missing atom types would cause grompp to fail; you'd never get to the point where a simulation would be affected. You're introducing custom atom types in the topology itself, and that's always legal before any [moleculetype] appears. The LJ parameters come from the [atomtypes] directive. Masses and charges present in that directive aren't used. Actually, to clarify: *if* masses are present in the [atoms] directive of a [moleculetype], then the masses found in [atomtypes] are not used. Strictly speaking, it is not necessary to have explicit masses in [atoms], though nearly all topologies do. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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. -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] Potential issue using acpype to convert amber topology to gromacs
Hi Justin, Many thanks for the detailed reply. I just wanted to check that it doesn't matter that the A2C and A3C are not present in the bonded and non-bonded itp files for the forcefield? Should this not have given an error? Kind regards, James From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul <jalem...@vt.edu> Sent: 14 February 2018 14:43:35 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Potential issue using acpype to convert amber topology to gromacs On 2/14/18 9:42 AM, Justin Lemkul wrote: > > > On 2/14/18 9:33 AM, Easton J.W. wrote: >> Thanks Justin, >> >> >> Will this effect the interactions (both bonded and non-bonded) that >> these atoms have, as their atom types are not in the forcefield itp >> files? > > Missing atom types would cause grompp to fail; you'd never get to the > point where a simulation would be affected. > > You're introducing custom atom types in the topology itself, and > that's always legal before any [moleculetype] appears. The LJ > parameters come from the [atomtypes] directive. Masses and charges > present in that directive aren't used. > Actually, to clarify: *if* masses are present in the [atoms] directive of a [moleculetype], then the masses found in [atomtypes] are not used. Strictly speaking, it is not necessary to have explicit masses in [atoms], though nearly all topologies do. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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. -- 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] Potential issue using acpype to convert amber topology to gromacs
On 2/14/18 9:42 AM, Justin Lemkul wrote: On 2/14/18 9:33 AM, Easton J.W. wrote: Thanks Justin, Will this effect the interactions (both bonded and non-bonded) that these atoms have, as their atom types are not in the forcefield itp files? Missing atom types would cause grompp to fail; you'd never get to the point where a simulation would be affected. You're introducing custom atom types in the topology itself, and that's always legal before any [moleculetype] appears. The LJ parameters come from the [atomtypes] directive. Masses and charges present in that directive aren't used. Actually, to clarify: *if* masses are present in the [atoms] directive of a [moleculetype], then the masses found in [atomtypes] are not used. Strictly speaking, it is not necessary to have explicit masses in [atoms], though nearly all topologies do. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] Potential issue using acpype to convert amber topology to gromacs
On 2/14/18 9:33 AM, Easton J.W. wrote: Thanks Justin, Will this effect the interactions (both bonded and non-bonded) that these atoms have, as their atom types are not in the forcefield itp files? Missing atom types would cause grompp to fail; you'd never get to the point where a simulation would be affected. You're introducing custom atom types in the topology itself, and that's always legal before any [moleculetype] appears. The LJ parameters come from the [atomtypes] directive. Masses and charges present in that directive aren't used. -Justin Kind regards, James From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul <jalem...@vt.edu> Sent: 14 February 2018 14:22:11 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Potential issue using acpype to convert amber topology to gromacs On 2/14/18 7:14 AM, Easton J.W. wrote: Hi, I've used acpype to convert my prmtop and inpcrd files into gromacs format. I'm using the amber14sb forcefield. At the top of the top file generated, is an [atomtypes] section. Most of the atoms in this section were present in the atomtypes.atp and ffnonbonded.itp so I deleted them however there were two atomtypes A2C and A3C that were not, so I left them. Looking back at my files after running some simulations I have realised that these were meant to be the 2C and 3C atomtypes, which had been converted. I've also realised that they do not have any mass in the atomtypes section. --- [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb A2C A2C 0.0 0.0 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 A3C A3C 0.0 0.0 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 [ moleculetype ] ;namenrexcl Peptide 3 [ atoms ] ; nr type resi res atom cgnr charge mass ; qtot bond_type 1N 1 CYS N1-0.415700 14.01000 ; qtot -0.416 2H 1 CYS H2 0.271900 1.00800 ; qtot -0.144 3 CX 1 CYSCA3 0.021300 12.01000 ; qtot -0.123 4 H1 1 CYSHA4 0.112400 1.00800 ; qtot -0.010 5 A2C 1 CYSCB5-0.123100 12.01000 ; qtot -0.133 6 H1 1 CYS HB26 0.111200 1.00800 ; qtot -0.022 7 H1 1 CYS HB37 0.111200 1.00800 ; qtot 0.089 8 SH 1 CYSSG8-0.311900 32.06000 ; qtot -0.223 9 HS 1 CYSHG9 0.193300 1.00800 ; qtot -0.029 10C 1 CYS C 10 0.597301 12.01000 ; qtot 0.568 11O 1 CYS O 11-0.567901 16.0 ; qtot -0.000 --- What will this mean for the simulations that I have run? The mass and charge information will be taken from [atoms], which always over-writes [atomtypes] for those quantities. So there should be no physical problem, e.g. from a "massless" atom. You can verify the masses by using gmx dump on your .tpr file and checking that they're non-zero for those atoms, but grompp would have failed before that point if they were truly massless. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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. -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] Potential issue using acpype to convert amber topology to gromacs
Thanks Justin, Will this effect the interactions (both bonded and non-bonded) that these atoms have, as their atom types are not in the forcefield itp files? Kind regards, James From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul <jalem...@vt.edu> Sent: 14 February 2018 14:22:11 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Potential issue using acpype to convert amber topology to gromacs On 2/14/18 7:14 AM, Easton J.W. wrote: > Hi, > > > I've used acpype to convert my prmtop and inpcrd files into gromacs format. > I'm using the amber14sb forcefield. > > > At the top of the top file generated, is an [atomtypes] section. Most of the > atoms in this section were present in the atomtypes.atp and ffnonbonded.itp > so I deleted them however there were two atomtypes A2C and A3C that were not, > so I left them. > > > Looking back at my files after running some simulations I have realised that > these were meant to be the 2C and 3C atomtypes, which had been converted. > I've also realised that they do not have any mass in the atomtypes section. > > > --- > > > [ atomtypes ] > ;name bond_type mass charge ptype sigma epsilon > Amb > A2C A2C 0.0 0.0 A 3.39967e-01 4.57730e-01 ; > 1.91 0.1094 > A3C A3C 0.0 0.0 A 3.39967e-01 4.57730e-01 ; > 1.91 0.1094 > > [ moleculetype ] > ;namenrexcl > Peptide 3 > > [ atoms ] > ; nr type resi res atom cgnr charge mass ; qtot > bond_type > 1N 1 CYS N1-0.415700 14.01000 ; qtot -0.416 > 2H 1 CYS H2 0.271900 1.00800 ; qtot -0.144 > 3 CX 1 CYSCA3 0.021300 12.01000 ; qtot -0.123 > 4 H1 1 CYSHA4 0.112400 1.00800 ; qtot -0.010 > 5 A2C 1 CYSCB5-0.123100 12.01000 ; qtot -0.133 > 6 H1 1 CYS HB26 0.111200 1.00800 ; qtot -0.022 > 7 H1 1 CYS HB37 0.111200 1.00800 ; qtot 0.089 > 8 SH 1 CYSSG8-0.311900 32.06000 ; qtot -0.223 > 9 HS 1 CYSHG9 0.193300 1.00800 ; qtot -0.029 > 10C 1 CYS C 10 0.597301 12.01000 ; qtot 0.568 > 11O 1 CYS O 11-0.567901 16.0 ; qtot -0.000 > > --- > > What will this mean for the simulations that I have run? The mass and charge information will be taken from [atoms], which always over-writes [atomtypes] for those quantities. So there should be no physical problem, e.g. from a "massless" atom. You can verify the masses by using gmx dump on your .tpr file and checking that they're non-zero for those atoms, but grompp would have failed before that point if they were truly massless. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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. -- 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] Potential issue using acpype to convert amber topology to gromacs
On 2/14/18 7:14 AM, Easton J.W. wrote: Hi, I've used acpype to convert my prmtop and inpcrd files into gromacs format. I'm using the amber14sb forcefield. At the top of the top file generated, is an [atomtypes] section. Most of the atoms in this section were present in the atomtypes.atp and ffnonbonded.itp so I deleted them however there were two atomtypes A2C and A3C that were not, so I left them. Looking back at my files after running some simulations I have realised that these were meant to be the 2C and 3C atomtypes, which had been converted. I've also realised that they do not have any mass in the atomtypes section. --- [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb A2C A2C 0.0 0.0 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 A3C A3C 0.0 0.0 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 [ moleculetype ] ;namenrexcl Peptide 3 [ atoms ] ; nr type resi res atom cgnr charge mass ; qtot bond_type 1N 1 CYS N1-0.415700 14.01000 ; qtot -0.416 2H 1 CYS H2 0.271900 1.00800 ; qtot -0.144 3 CX 1 CYSCA3 0.021300 12.01000 ; qtot -0.123 4 H1 1 CYSHA4 0.112400 1.00800 ; qtot -0.010 5 A2C 1 CYSCB5-0.123100 12.01000 ; qtot -0.133 6 H1 1 CYS HB26 0.111200 1.00800 ; qtot -0.022 7 H1 1 CYS HB37 0.111200 1.00800 ; qtot 0.089 8 SH 1 CYSSG8-0.311900 32.06000 ; qtot -0.223 9 HS 1 CYSHG9 0.193300 1.00800 ; qtot -0.029 10C 1 CYS C 10 0.597301 12.01000 ; qtot 0.568 11O 1 CYS O 11-0.567901 16.0 ; qtot -0.000 --- What will this mean for the simulations that I have run? The mass and charge information will be taken from [atoms], which always over-writes [atomtypes] for those quantities. So there should be no physical problem, e.g. from a "massless" atom. You can verify the masses by using gmx dump on your .tpr file and checking that they're non-zero for those atoms, but grompp would have failed before that point if they were truly massless. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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.
