[gmx-users] ligand parameters (was Re: gmx-users Digest, Vol 79, Issue 114)

[Justin A. Lemkul]

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ITHAYARAJA wrote:
> Dear Sir,
> 
> Greetings!
> 
> It may be basic question but it is very important to go further, my 
> doubt is,
> 
> My protein is soluble form with three ligand and two of them are hetatm 
> (FAD and NADPH) i would like study the substrate, hetatm ligand 
> simulation by gromacs. please make clear to understand and how to do my 
> hetatm to pdb file
> 

HETATM entries are handled by Gromacs, provided that these residues are 
described in the .rtp file.  Some force fields have parameters for cofactors 
like FAD and NADP, but not all.  Your substrate is far less likely to be already 
built into your force field, requiring careful parameterization.

http://www.gromacs.org/Documentation/How-tos/Parameterization

This is a complex task, and you will need a thorough understanding of the 
underlying mechanics of your chosen force field and the methods by which it was 
derived.  A couple of hours of careful reading will save you a couple of months 
of generating meaningless data.

-Justin

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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