[gmx-users] converting pdb file to gromacs input file
Subashini .K
subashinik at hotmail.com
Sat Jan 14 11:05:00 CET 2017
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
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