[gmx-users] Protein-ligand opls ff

Justin Lemkul jalemkul at vt.edu
Tue Feb 21 19:04:11 CET 2017

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 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


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