[gmx-users] question

Justin Lemkul jalemkul at vt.edu
Tue May 12 13:30:09 CEST 2015

On 5/12/15 12:36 AM, Andrew Bostick wrote:
> Dear Justin
> Very thanks for your answer
> I should use my pdb file in which there is no bond between CD atom of GLU
> residue from peptide 1 and NZ atom of LYS residue from peptide 2. Creating
> new entry in specbond.dat file will consider this new bond. Is my vision
> true?
> Based on your answer, only thing I should do is creating a new entry in
> specbond.dat? Should I don't other thing?

As I said, you need a new entry in specbond.dat and special .rtp entries.

> Based on following link (
> http://www.gromacs.org/Documentation/File_Formats/specbond.dat), my new
> entry is as follows, is it true?
> GLU     CD      1       LYS     NZ      1       0.13     GLU2    LYS2
> How to get the  accurate reference length for searching for candidate bonds?

Well, what should be the C-N bond length in a normal peptide bond?

> In my system there is more than 1 Lys and 1 Glu residues. I want this new
> bond between special residue of  Lys (for example number: 28 ) and special
> residue of Glu (for example number: 45). How to set this state in
> specbond.dat file?

This is what the distance column is for; special linkages are only created if 
the distance between the specified atoms is within 10% of that criterion.



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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