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
>
> ==
>
> --
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--
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)
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