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

[Justin Lemkul]

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

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Justin A. Lemkul, Ph.D.
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