[gmx-users] Unit of force constants and adding new residue.

Justin Lemkul jalemkul at vt.edu
Wed Jun 25 12:01:36 CEST 2014

On 6/25/14, 4:42 AM, Dawid das wrote:
> Dear Gromacs experts,
> I have a few questions regarding adding a new residue to the force field.
> 1) In what unit should provide force constants for stretching, bending and
> torsion in aminoacids.rtp file? I can't really figure that out from gromacs
> manual.

See table 5.5 in the manual; all units are listed there for all interaction types.

> 2) If I provide those constants and natural values of bond lengths, angles,
> etc.  in aminoacids.rtp file, do I need to provide them in ffbonded.itp?

No, values can be taken directly from the .rtp and written to the .top

> 3) My new residue has to be connected with two natural aminoacids (Phe,
> Gly, etc.). Where do I specify the parameters for new atom types (of my
> new  residue) and for these "regular" atom types? For example, torsion or
> stretching paramters where those two residues are connected.

Bonded parameters should be listed in ffbonded.itp.


> What I want to do exactly is to add parameters from Tinker format FF for a
> chromophore of mCherry fluorescent protein. I try to do things according to
> this manual:
> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
> I will be grateful for any help :).
> Best wishes,
> Dawid Grabarek


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


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