[gmx-users] use of PRODRG

[Justin Lemkul]

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: jalemkul at vt.edu
>> To: gmx-users at 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

========================================