[gmx-users] Protein-ligand opls ff

[Chetan Puri]

I am from Organic chemistry background and I don't know much about
inorganic chemistry calculations.

So I would request you if you could guide me , how to generate a topology
file for a small molecule.  e.g. ATP or benzoic acid for OPLS ff
On 21 Feb 2017 11:34 pm, "Justin Lemkul" <jalemkul at vt.edu> wrote:



On 2/21/17 12:56 PM, Jonathan Saboury wrote:

> I'm very inexperienced, so probably shouldn't be giving advice, but I think
> the below is correct :)
>
> Justin Lemkul has made many tutorials that have been invaluable to me.
> Below is his tutorial on how to prepare such a system using the GROMOS96
> 43A1 force field. (This can be changed to OPLS-AA/L all-atom force field
> during the "gmx pdb2gmx -f 3HTB_clean.pdb -o 3HTB_processed.gro -water spc"
> step.)
>
>
OPLS/AA + SPC is not a combination that I'm aware of as having been tested.
TIP3P or SPC/E should be used with OPLS/AA based on the original
parametrization (TIP3P) and a published systematic analysis of hydration
free energies of amino acid analogues (SPC/E), respectively.

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx
> -tutorials/complex/index.html
>
>
In general, the protocol is the same, but beware the details.


Since you already have your ligand .top file you just need to copy and
> paste the ligand.itp line from that .top to your new one.
>
>
I believe the question was in reference to how one would produce the
topology file for the ligand.  If one already has it, of course proceeding
is trivial. Perhaps the OP can clarify the nature of the difficulty.  There
are a number of tools and scripts for creating OPLS/AA ligand topologies
(just a Google search away!), but of course there is no substitute for
careful examination of the literature, which for OPLS/AA is going to
require some understanding of QM calculations in the event that
corresponding or analogous parameters are not already available.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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