[gmx-users] question

Justin Lemkul jalemkul at vt.edu
Mon May 11 22:43:17 CEST 2015

On 5/11/15 2:34 PM, Andrew Bostick wrote:
> Dear gromacs users
> I have experience in MD simulation of protein and peptides by gromos force
> field.
> Now I am working on a new project in which I should connect two peptides
> (based on experimental data) to obtain one new peptide. This connection is
> as follows:
> CD atom of GLU residue from peptide 1 and NZ atom of LYS residue from
> peptide 2.
> 1) How to make this connection (which software) to gromacs recognize this
> new state.

Create a new entry in specbond.dat.

> 2) Should I need to change force field parameters?

This is just a peptide bond; all force fields will have the needed parameters.

> 3) Should I define new residue containing Glu-Lys?

You need two residues, one for a special Lys, one for a special Glu, edited to 
reflect the new side chain chemical groups and any subsequent adjustments to 
charge and atom type.  The new residue names are part of what you specify in 



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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