[gmx-users] validation of ligand parametrization

Justin A. Lemkul jalemkul at vt.edu
Wed Jan 26 12:44:42 CET 2011

mohsen ramezanpour wrote:
> Dear All and specially Dear Dr.Justin
> I generated parameters for a typical ligand.
> now I want to validate it.
> How can I do it?
> Please let me know references for doing this.
> Of course I have read the article by Dr.Justin(Alzeimer),Unfortunately I 
> couldn't understand it completely and very good.

I will assume that you're still using one of the Gromos force fields for your 
work.  Gromos parameterization relies on reproduction of condensed-phase 
behavior, in theory, the partitioning of the species of interest between 
hydrophobic and aqueous media.  Ideally, you would calculate deltaG of hydration 
in different media, but such information is not always readily available. 
That's why I turned to an alternate approach in the paper you mention, but one 
that holds in the same spirit of the force field and for which I had 
experimental evidence with which to compare.

If you don't have any suitable experimental data regarding your ligand, you 
should re-evaluate your force field choice and consider whether or not 
parameterizing a bunch of unknown compounds is a viable approach.

I certainly cannot help you better if you simply say you don't understand 
something.  What isn't clear?

> Is there any other article who has done validation after parametrization?

Some, but (unfortunately) not many.  Numerous authors seem to blindly rely on 
PRODRG, which was the motivation behind our most recent work (in JCIM, which I 
believe you said you've read).  See the references therein for a few examples of 
attempts that have been made to derive and validate proper parameters.  More 
rigorous standards are really necessary to avoid potential inaccuracies in these 
types of simulations.


> Thanks in advance for your guidance.


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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