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
> 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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