[gmx-users] topology file of ligand

[Justin Lemkul]

On 10/15/13 11:24 AM, sunyeping wrote:
> Dear gromacs users,
>
> I am study the tutorial for protein-ligand complex system (gromacs tutorial 5: T4 lysozyme in complex with JZ4). The tutorial use PRODRG to produce the topology file. The author state that he  immediately notice three things that are wrong with this topology, which include charge group, H atom charge, etc.
>       And the author then reconstructed a topology file.  I don't understand how the charge group and charge of individual atom are correctly assigned. Could you explain it to me?
>

The Gromos96 parameter sets assign charges and charge groups based on chemical 
functional groups that are transferable between molecules.  Spotting 
inaccuracies and knowing how to fix them come with understanding how the force 
field was derived (read the primary literature and study existing molecules).

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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