[gmx-users] PRODRG

[Justin Lemkul]

On 7/16/14, 1:42 AM, Sarath Kumar Baskaran wrote:
> Dear all,
>
> I was using PRODRG for my protein ligand Simulations,
> Later, I came across the issues of PRODRG topologies on atom charges, and i
> have been tryiing to correct these problems.
> I couldnt use ATB since it gives topopology only for GROMOS96 53a5 and 53a6
> force field
> whereas i need for GROMOS96 43a1.
> There is a program - ITP Adjuster, an utiltity to correct these charges.
>
> Journal of Chemistry
> ​ - ​
> Volume 2013 (2013), Article ID 803151, 6 pages
> ITP Adjuster 1.0: A New Utility Program to Adjust Charges in the Topology
> Files Generated by the PRODRG Server.
> ​
>   http://dx.doi.org/10.1155/2013/803151​
>
> *​*Is it wise to use this program
> ​ to correct the PRODRG output​
> ?

Looking briefly through that paper, it seems that the charges are somewhat 
over-fitted, and in some cases very different from the existing functional 
groups in the force field.  The "validation" they provide simply states that 
their program changed the charges; it doesn't demonstrate that the topologies 
are sane.

QM calculations are the first, but not final, step in deriving Gromos-compatible 
topologies.  You can piece together most molecules from existing functional 
groups; transferability is at the heart of any force field, particularly one 
built in pieces as the Gromos parameter sets have been.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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
http://mackerell.umaryland.edu/~jalemkul

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