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

[Paolo Costa]

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?

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)