Re: [gmx-users] Problem C-H bonds of Benzene after minimization
Hi Justin, indeed there are only six bonds in the topology files! As you said the hydrogen nomenclature in .rtp file is wrong. Thanks a lot! Paolo Il giorno gio 23 apr 2020 alle ore 12:55 Justin Lemkul ha scritto: > > > On 4/23/20 6:52 AM, Paolo Costa wrote: > > Dear Gromacs Users, > > > > I am trying to perform MD simulations of benzene molecule in a cube of > > water just for practicing. > > By following the tutorial > > https://www.svedruziclab.com/tutorials/gromacs/2-methane-in-water/, I > setup > > the residue Benzene within Amber99 force field. After the minimization > > however I got the C-H bonds of benzene distorted and unusually stretched. > > During the grompp procedure I got the following note: > > > > " In moleculetype 'Other' 6 atoms are not bound by a potential or > >constraint to any other atom in the same moleculetype. Although > >technically this might not cause issues in a simulation, this often > means > >that the user forgot to add a bond/potential/constraint or put > multiple > >molecules in the same moleculetype definition by mistake. Run with -v > to > >get information for each atom." > > > > Could it be related to the problem I am facing? > > > > Here the starting .pdb file of benzene: > > COMPNDBENZENE > > REMARK1 File created by GaussView 6.0.16 > > HETATM1 C1 C6H6 0 0.968 1.903 0.000 >C > > HETATM2 C2 C6H6 0 2.363 1.903 0.000 >C > > HETATM3 C3 C6H6 0 3.060 3.111 0.000 >C > > HETATM4 C4 C6H6 0 2.363 4.319 -0.001 >C > > HETATM5 C5 C6H6 0 0.968 4.319 -0.002 >C > > HETATM6 C6 C6H6 0 0.270 3.111 -0.001 >C > > HETATM7 H1 C6H6 0 0.418 0.951 0.000 >H > > HETATM8 H2 C6H6 0 2.912 0.951 0.001 >H > > HETATM9 H3 C6H6 0 4.160 3.111 0.001 >H > > HETATM 10 H4 C6H6 0 2.913 5.272 -0.001 >H > > HETATM 11 H5 C6H6 0 0.418 5.272 -0.003 >H > > HETATM 12 H6 C6H6 0 -0.829 3.111 -0.001 >H > > END > > CONECT1267 > > CONECT2138 > > CONECT3249 > > CONECT435 10 > > CONECT546 11 > > CONECT615 12 > > CONECT71 > > CONECT82 > > CONECT93 > > CONECT 104 > > CONECT 115 > > CONECT 126 > > > > Here the .rtp file included in Amber99.ff: > > [ C6H6 ] > > [ atoms ] > > C1 CA -0.1285 1 > > C2 CA -0.1285 2 > > C3 CA -0.1285 3 > > C4 CA -0.1285 4 > > C5 CA -0.1285 5 > > C6 CA -0.1285 6 > > H1 HA0.1285 7 > > H2 HA0.1285 8 > > H3 HA0.1285 9 > > H4 HA0.1285 10 > > H5 HA0.1285 11 > > H6 HA0.1285 12 > > [ bonds ] > > C1 H7 > > C1 C2 > > C1 C6 > > C2 C8 > > C2 C1 > > C2 C3 > > C3 H9 > > C3 C2 > > C3 C4 > > C4 H10 > > C4 C3 > > C4 C5 > > C5 H11 > > C5 C4 > > C5 C6 > > C6 H12 > > C6 C5 > > C6 C1 > > > > Can somebody help me to figure out such issue? > > The bonds in the .rtp file are wrong. The hydrogen nomenclature is > incorrect so you do not have any C-H bonds in the topology. You can > verify this for yourself. You probably have 6 bonds instead of 12. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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. > -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) -- 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] Problem C-H bonds of Benzene after minimization
On 4/23/20 6:52 AM, Paolo Costa wrote: Dear Gromacs Users, I am trying to perform MD simulations of benzene molecule in a cube of water just for practicing. By following the tutorial https://www.svedruziclab.com/tutorials/gromacs/2-methane-in-water/, I setup the residue Benzene within Amber99 force field. After the minimization however I got the C-H bonds of benzene distorted and unusually stretched. During the grompp procedure I got the following note: " In moleculetype 'Other' 6 atoms are not bound by a potential or constraint to any other atom in the same moleculetype. Although technically this might not cause issues in a simulation, this often means that the user forgot to add a bond/potential/constraint or put multiple molecules in the same moleculetype definition by mistake. Run with -v to get information for each atom." Could it be related to the problem I am facing? Here the starting .pdb file of benzene: COMPNDBENZENE REMARK1 File created by GaussView 6.0.16 HETATM1 C1 C6H6 0 0.968 1.903 0.000 C HETATM2 C2 C6H6 0 2.363 1.903 0.000 C HETATM3 C3 C6H6 0 3.060 3.111 0.000 C HETATM4 C4 C6H6 0 2.363 4.319 -0.001 C HETATM5 C5 C6H6 0 0.968 4.319 -0.002 C HETATM6 C6 C6H6 0 0.270 3.111 -0.001 C HETATM7 H1 C6H6 0 0.418 0.951 0.000 H HETATM8 H2 C6H6 0 2.912 0.951 0.001 H HETATM9 H3 C6H6 0 4.160 3.111 0.001 H HETATM 10 H4 C6H6 0 2.913 5.272 -0.001 H HETATM 11 H5 C6H6 0 0.418 5.272 -0.003 H HETATM 12 H6 C6H6 0 -0.829 3.111 -0.001 H END CONECT1267 CONECT2138 CONECT3249 CONECT435 10 CONECT546 11 CONECT615 12 CONECT71 CONECT82 CONECT93 CONECT 104 CONECT 115 CONECT 126 Here the .rtp file included in Amber99.ff: [ C6H6 ] [ atoms ] C1 CA -0.1285 1 C2 CA -0.1285 2 C3 CA -0.1285 3 C4 CA -0.1285 4 C5 CA -0.1285 5 C6 CA -0.1285 6 H1 HA0.1285 7 H2 HA0.1285 8 H3 HA0.1285 9 H4 HA0.1285 10 H5 HA0.1285 11 H6 HA0.1285 12 [ bonds ] C1 H7 C1 C2 C1 C6 C2 C8 C2 C1 C2 C3 C3 H9 C3 C2 C3 C4 C4 H10 C4 C3 C4 C5 C5 H11 C5 C4 C5 C6 C6 H12 C6 C5 C6 C1 Can somebody help me to figure out such issue? The bonds in the .rtp file are wrong. The hydrogen nomenclature is incorrect so you do not have any C-H bonds in the topology. You can verify this for yourself. You probably have 6 bonds instead of 12. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] Problem C-H bonds of Benzene after minimization
Dear Gromacs Users, I am trying to perform MD simulations of benzene molecule in a cube of water just for practicing. By following the tutorial https://www.svedruziclab.com/tutorials/gromacs/2-methane-in-water/, I setup the residue Benzene within Amber99 force field. After the minimization however I got the C-H bonds of benzene distorted and unusually stretched. During the grompp procedure I got the following note: " In moleculetype 'Other' 6 atoms are not bound by a potential or constraint to any other atom in the same moleculetype. Although technically this might not cause issues in a simulation, this often means that the user forgot to add a bond/potential/constraint or put multiple molecules in the same moleculetype definition by mistake. Run with -v to get information for each atom." Could it be related to the problem I am facing? Here the starting .pdb file of benzene: COMPNDBENZENE REMARK1 File created by GaussView 6.0.16 HETATM1 C1 C6H6 0 0.968 1.903 0.000 C HETATM2 C2 C6H6 0 2.363 1.903 0.000 C HETATM3 C3 C6H6 0 3.060 3.111 0.000 C HETATM4 C4 C6H6 0 2.363 4.319 -0.001 C HETATM5 C5 C6H6 0 0.968 4.319 -0.002 C HETATM6 C6 C6H6 0 0.270 3.111 -0.001 C HETATM7 H1 C6H6 0 0.418 0.951 0.000 H HETATM8 H2 C6H6 0 2.912 0.951 0.001 H HETATM9 H3 C6H6 0 4.160 3.111 0.001 H HETATM 10 H4 C6H6 0 2.913 5.272 -0.001 H HETATM 11 H5 C6H6 0 0.418 5.272 -0.003 H HETATM 12 H6 C6H6 0 -0.829 3.111 -0.001 H END CONECT1267 CONECT2138 CONECT3249 CONECT435 10 CONECT546 11 CONECT615 12 CONECT71 CONECT82 CONECT93 CONECT 104 CONECT 115 CONECT 126 Here the .rtp file included in Amber99.ff: [ C6H6 ] [ atoms ] C1 CA -0.1285 1 C2 CA -0.1285 2 C3 CA -0.1285 3 C4 CA -0.1285 4 C5 CA -0.1285 5 C6 CA -0.1285 6 H1 HA0.1285 7 H2 HA0.1285 8 H3 HA0.1285 9 H4 HA0.1285 10 H5 HA0.1285 11 H6 HA0.1285 12 [ bonds ] C1 H7 C1 C2 C1 C6 C2 C8 C2 C1 C2 C3 C3 H9 C3 C2 C3 C4 C4 H10 C4 C3 C4 C5 C5 H11 C5 C4 C5 C6 C6 H12 C6 C5 C6 C1 Can somebody help me to figure out such issue? Thanks. Paolo -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) -- 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.