[gmx-users] converting pdb file to gromacs input file

[Subashini .K]

Hi gromacs users,


I am a new gromacs user.


I wanted to generate a .gro, .itp, .conf file using the command


$ gmx pdb2gmx -f lig.pdb


However, the pdb file must be in the required format.

What should we type instead of LIG corresponding to each and every atom?


This is an example file of phenylcyclohexane.

Please tell me how to proceed further?


COMPND    Phenylcyclohexane
AUTHOR    GENERATED BY OPEN BABEL 2.3.2
HETATM    1  C   LIG     1      -2.801   1.177   0.180  1.00  0.00           C
HETATM    2  C   LIG     1      -1.406   1.177   0.180  1.00  0.00           C
HETATM    3  C   LIG     1      -0.708   2.371   0.000  1.00  0.00           C
HETATM    4  C   LIG     1      -1.405   3.566  -0.181  1.00  0.00           C
HETATM    5  C   LIG     1      -2.800   3.566  -0.181  1.00  0.00           C
HETATM    6  C   LIG     1      -3.498   2.372  -0.001  1.00  0.00           C
HETATM    7  H   LIG     1      -3.350   0.236   0.322  1.00  0.00           H
HETATM    8  H   LIG     1      -0.856   0.235   0.323  1.00  0.00           H
HETATM    9  H   LIG     1      -0.855   4.508  -0.323  1.00  0.00           H
HETATM   10  H   LIG     1      -3.350   4.508  -0.324  1.00  0.00           H
HETATM   11  H   LIG     1      -4.598   2.372  -0.001  1.00  0.00           H
HETATM   12  C   LIG     1       0.832   2.372   0.001  1.00  0.00           C
HETATM   13  C   LIG     1       1.339   1.686   1.253  1.00  0.00           C
HETATM   14  C   LIG     1       1.341   1.681  -1.248  1.00  0.00           C
HETATM   15  H   LIG     1       1.170   3.441  -0.001  1.00  0.00           H
HETATM   16  C   LIG     1       2.852   1.589   1.256  1.00  0.00           C
HETATM   17  H   LIG     1       0.900   0.655   1.317  1.00  0.00           H
HETATM   18  H   LIG     1       0.998   2.254   2.157  1.00  0.00           H
HETATM   19  C   LIG     1       2.853   1.585  -1.246  1.00  0.00           C
HETATM   20  H   LIG     1       0.902   0.650  -1.309  1.00  0.00           H
HETATM   21  H   LIG     1       1.002   2.245  -2.155  1.00  0.00           H
HETATM   22  C   LIG     1       3.361   0.900   0.006  1.00  0.00           C
HETATM   23  H   LIG     1       3.190   1.023   2.162  1.00  0.00           H
HETATM   24  H   LIG     1       3.291   2.620   1.318  1.00  0.00           H
HETATM   25  H   LIG     1       3.194   1.016  -2.150  1.00  0.00           H
HETATM   26  H   LIG     1       3.291   2.615  -1.311  1.00  0.00           H
HETATM   27  H   LIG     1       4.482   0.903   0.007  1.00  0.00           H
HETATM   28  H   LIG     1       3.027  -0.170   0.008  1.00  0.00           H

Thanks,
Subashini.K