[gmx-users] validation of ligand parametrization

mohsen ramezanpour ramezanpour.mohsen at gmail.com
Wed Jan 26 13:10:15 CET 2011

Dear Justin
I don't want to rely on PRODRG server as others.
I want to do my work as accurate as possible.
Absolutely I read your papar and I know PRODRG present bad results for
estimating free energies.
I want to parametrize my drugs by GROMOS43A1 parameters as you said.
I know completely how to do it.Thanks for your and other user's guidances.
Actually I couldn't find any experimentally data to try to obtain it's
result.Then i have to
do what you said.(re-evaluating force field choice and .....)
Can you please say me more about this method?
Did you have something like this in your papers?
Thanks in advance for your reply

On Wed, Jan 26, 2011 at 3:14 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> 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.
> -Justin
>  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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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