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.
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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