[gmx-users] Adding new residue - modified LYS

Justin Lemkul jalemkul at vt.edu
Sun Jan 15 18:54:12 CET 2017

On 1/14/17 2:38 PM, Dan Si wrote:
> Hi,
> I'm struggling with adding a new residue to my MD simulation. I would like
> to create a residue (let's call it NML) that would be an original lysine
> (LYS) residue with methyl group attached to it's amide bond nitrogen. I'm
> using amber99sb-ildn force field for my simulations. Unfortunately, I'm very
> new in using gromacs, so I would appreciate really !step-by-step! tutorial :
> -)
> Do I need to perform QM calculation to obtain some of the parameters? If
> yes, should I use zwitter-ionic structure NH3-CH-(R)-C-(O)-O in the
> optimization?

What do you learn from reading the AMBER99sb-ILDN paper (and preceding 
literature) regarding AMBER parametrization methodology?

> I understand, I need to specify the topology of the new residue and
> parameters according to amber99sb-ildn force field, but how exactly am I
> suppose to do it? Which files I need to modify before running pdb2gmx and
> how?




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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