[gmx-users] Problem C-H bonds of Benzene after minimization

[Paolo Costa]

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 <jalemkul at vt.edu> 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:
> > COMPND    BENZENE
> > REMARK    1 File created by GaussView 6.0.16
> > HETATM    1  C1  C6H6  0       0.968   1.903   0.000
>    C
> > HETATM    2  C2  C6H6  0       2.363   1.903   0.000
>    C
> > HETATM    3  C3  C6H6  0       3.060   3.111   0.000
>    C
> > HETATM    4  C4  C6H6  0       2.363   4.319  -0.001
>    C
> > HETATM    5  C5  C6H6  0       0.968   4.319  -0.002
>    C
> > HETATM    6  C6  C6H6  0       0.270   3.111  -0.001
>    C
> > HETATM    7  H1  C6H6  0       0.418   0.951   0.000
>    H
> > HETATM    8  H2  C6H6  0       2.912   0.951   0.001
>    H
> > HETATM    9  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
> > CONECT    1    2    6    7
> > CONECT    2    1    3    8
> > CONECT    3    2    4    9
> > CONECT    4    3    5   10
> > CONECT    5    4    6   11
> > CONECT    6    1    5   12
> > CONECT    7    1
> > CONECT    8    2
> > CONECT    9    3
> > CONECT   10    4
> > CONECT   11    5
> > CONECT   12    6
> >
> > 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   HA    0.1285  7
> > H2   HA    0.1285  8
> > H3   HA    0.1285  9
> > H4   HA    0.1285  10
> > H5   HA    0.1285  11
> > H6   HA    0.1285  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
>
> jalemkul at 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)