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 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ; > 1.91 0.1094 > A3C A3C 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ; > 1.91 0.1094 > > [ moleculetype ] > ;name nrexcl > Peptide 3 > > [ atoms ] > ; nr type resi res atom cgnr charge mass ; qtot > bond_type > 1 N 1 CYS N 1 -0.415700 14.01000 ; qtot -0.416 > 2 H 1 CYS H 2 0.271900 1.00800 ; qtot -0.144 > 3 CX 1 CYS CA 3 0.021300 12.01000 ; qtot -0.123 > 4 H1 1 CYS HA 4 0.112400 1.00800 ; qtot -0.010 > 5 A2C 1 CYS CB 5 -0.123100 12.01000 ; qtot -0.133 > 6 H1 1 CYS HB2 6 0.111200 1.00800 ; qtot -0.022 > 7 H1 1 CYS HB3 7 0.111200 1.00800 ; qtot 0.089 > 8 SH 1 CYS SG 8 -0.311900 32.06000 ; qtot -0.223 > 9 HS 1 CYS HG 9 0.193300 1.00800 ; qtot -0.029 > 10 C 1 CYS C 10 0.597301 12.01000 ; qtot 0.568 > 11 O 1 CYS O 11 -0.567901 16.00000 ; 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.
