On 9/19/12 11:40 AM, Elie M wrote:
I don't understand this. PRODRG will be of no use here since you are using
OPLS-AA, and if there is no ligand, then why do you need some external program
to build a topology?
- The "LIG" residue only appears in the pdb version of the file. I tried to
use editconf on the .mol type of file to change into .gro file but it gave an error so I
thought editconf only changes pdb files into .gro ones. This raises a question: What
other types of files does editconf change into .gro? Anyways, this is a part of the .mol
file produced by Marvin Sketch:
There is a list (somewhat cryptic if you're not used to reading it) in
src/gmxlib/filenm.c, which would suggest a variety of formats are acceptable,
but not .mol2 files. Most of the common ones (and some more exotic) can be
used: .pdb, .gro, .g96, .g87, .brk, .pqr, .xyz, .ent, .esp, and perhaps a few
more, just based on a quick scan.
-Justin
Mrv0541 09081217542D
46 50 0 0 0 0 999 V2000 5.3375 -1.9029 0.0000 C 0 0
0 0 0 0 0 0 0 0 0 0 5.7500 -2.6174 0.0000 C 0 0 0 0 0
0 0 0 0 0 0 0 5.1979 -3.2305 0.0000 S 0 0 0 0 0 0 0 0 0
0 0 0 4.4443 -2.8949 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.5305 -2.0744 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0153
-2.8949 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7298 -3.3074
0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7298 -4.1324 0.0000 C
0 0 0 0 0 0 0 0 0 0 0 0 3.0153 -4.5449 0.0000 C 0 0 0 0
0 0 0 0 0 0 0 0 2.3008 -4.1324 0.0000 C 0 0 0 0 0 0 0
0 0 0 0 0 2.3008 -3.3074 0.0000 C 0 0 0 0 0 0 0 0 0 0 0
0 0.8327 -4.2093 0.0000 S 0 0 0 0 0 0 0 0 0 0 0
0..........
Thanks for your help
Elie
Date: Wed, 19 Sep 2012 05:23:28 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] use of PRODRG
On 9/18/12 10:35 PM, Elie M wrote:
Dear all,
I have been reading about PRODRG that takes a PDB file as an input and produces
topologies compatible with GROMACS as an output. Can this program be then
considered as a solution to the problem of missing residues in GROMACS like LIG?
PRODRG produces topologies for the Gromos96 43a1 parameter set (and an older
version produces topologies for the outdated Gromos87), and the quality of the
topologies is generally very low. The resulting topologies require significant
modification.
N.B: I am using the OPLSAA force field .I also have the files in MDL MOL2
version which do not contain the LIG residue appearing in the PDB file. So
maybe using PRODRG on the MOL2 might solve the problem?
I don't understand this. PRODRG will be of no use here since you are using
OPLS-AA, and if there is no ligand, then why do you need some external program
to build a topology?
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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