[gmx-users] converting pdb file to gromacs input file
Subashini .K
subashinik at hotmail.com
Sat Jan 14 12:01:53 CET 2017
It says, RESIDUE NOT FOUND in residue topology database
For example in methane, the example was
COMPND METHANE
AUTHOR GENERATED BY OPEN BABEL 2.3.2
HETATM 1 C CH4 1 -0.370 0.900 0.000 1.00 0.00 C
HETATM 2 H1 CH4 1 0.700 0.900 0.000 1.00 0.00 H
HETATM 3 H2 CH4 1 -0.727 0.122 0.643 1.00 0.00 H
HETATM 4 H3 CH4 1 -0.727 0.731 -0.995 1.00 0.00 H
HETATM 5 H4 CH4 1 -0.727 1.845 0.351 1.00 0.00 H
END
What does CH4 mean here?
Then, should we mention the hybridization of each and every atom?
________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Sotirios Dionysios I. Papadatos <si.papadatos at edu.cut.ac.cy>
Sent: Saturday, January 14, 2017 4:06 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] converting pdb file to gromacs input file
In pdb2gmx you give as an input the filename.pdb. This should do the trick. But I think there is something else that you truly need. Maybe you need some more info on how to add a hetatm in an existing force field.?
________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Subashini .K <subashinik at hotmail.com>
Sent: Saturday, January 14, 2017 12:04:40 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] converting pdb file to gromacs input file
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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