[gmx-users] Ligand charge assignment

[Mark Abraham]

On 21/11/2011 9:28 PM, archana sonawani wrote:
> Dear Sir/madam,
>
> I have a ligand molecule for which I generated the topology file using 
> Prodrg software. As the charges and groupings provided by Prodrg are 
> not much reliable. I need to assign correct charges and groupings for 
> my ligand. I had referred the article "Practical considerations for 
> building GROMOS-compatible small-molecule topologies". I could assign 
> charges and groupings for most of the molecule except for the 
> heterocyclic structures and sulfur atom in ring. Please help me 
> out...Thanks in advance..
>

Welcome to the jungle. :-) Paramterization is an expert topic for a 
reason. You should search the literature to find what approaches have 
been used for such heteroatoms and see what might be applicable to your 
case. Regardless, you will need to demonstrate that your parameters do a 
decent job on some known experimental data before they can be supposed 
to have value for a computational study.

Mark
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