[gmx-users] building a new molecule which does not exist in gmx data base

[Justin A. Lemkul]

shivangi nangia wrote:
> Dear Justin and other gmx-users,
> 
> As per the journal article, Practical Considerations for Building 
> GROMOS-Compatible Small-Molecule Topologies, PRODRG 2.5 server does not 
> assign  charges compatible with GROMOS force field.
> PRODRG 2.5, however, assigns the correct atom types and bonded parameters.
> 
> I have to build 2,5-dihydroxybenzoic acid
> 
> Starting from PRODRG 2.5 produced .itp and further rectification is a 
> good idea? If yes, what should be strategy?
> 

As we state in the article, the topology provided by PRODRG is a reasonable 
template, but the charges and charge groups require modification.  I've never 
seen a PRODRG topology that was correct at face value.  That said, with adequate 
modification, the topology should be reasonable for use with Gromos96 43a1; 
other modifications (atom types, etc) may be necessary to make the topology 
compatible with other, more modern, Gromos96 parameter sets.

> And if PRODRG should not be my starting point at all, then how should I 
> go about building the molecule/anion.
> 
> 
> Please guide, as I am not well versed with gromacs.
> 

For a molecule like yours, assigning charges and charge groups by analogy to 
existing functional groups should be a simple exercise.  If this does not give a 
satisfactory result (based on validation methods discussed in the literature), 
then apply the charge calculations described in our article.  Note that this 
task must be done with software external to Gromacs.

If you are not very comfortable with these ideas, it is not wise to plow ahead 
blindly and hope for the best.  Parameterization is an expert topic for a 
reason.  It requires great care and a thorough understanding of the intrinsic 
features of the force field you wish to work with.

-Justin

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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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