[gmx-users] Modified peptides

Justin Lemkul jalemkul at vt.edu
Sat Apr 2 19:04:37 CEST 2016

On 4/2/16 2:11 AM, sun wrote:
> Hello Gromacs Users I have already posted this query but in the absence of
> any suggestion, I am posting it again. I hope someone will help me. I am
> going to do protein-peptide MD using Justin's protein-ligand tutorial (ff
> gromos43A1, GROMACS version 5.0). My ligand is a pentameric modified peptide.
> In the tutorial, I studied that Gromos96 parameters are obtained from PRODRG
> server but due to less uniformity in charges, it is not 100% reliable. Its
> allright, Charges can be corrected from the paper that is cited in tutorial.
> But, I have also read that for modified peptides or sequences, we can make
> changes in force fields manually. So, my query is, which option would be more
> suitable for my peptide? Is it OK to obatin co-ordinates for modified amino
> acid from PRODRG?

You don't need PRODRG at all, really, but sure, you can use coordinates.

The proper answer is to parametrize the residue in a manner consistent with the 
parent force field.  The downside to GROMOS force fields is that, while the 
functional groups are generally quite transferable, coming up with new 
parameters is hard.  The published papers do not give many methodological 
details, rather emphasizing the empirical nature of the force field.  This 
implies that one needs an intuitive sense of how to parameterize new species, 
which is both frustrating to new users and unsatisfying in a rigorous sense. 
Force fields like CHARMM, AMBER, and OPLS-AA have very easy-to-follow, logical 
progression from QM calculations for initial electrostatic parameters and 
internal terms, to empirical refinement based on very well defined criteria.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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