[gmx-users] s-s bond recognition

[Justin Lemkul]

On 11/23/14 8:26 AM, Hamid Mahdiuni wrote:
> Hi everyone
> I’m going to run -pdb2gmx on my protein with PDB code of 2O6X. This protein
> has three S-S bonds within its crystal structure, but, after running of
> -pdb2gmx, only 2 of them recognized as S-S bond. I think that the distance
> between S atom of Cys253 and its counterpart of Cys302 is too long to form
> S-S bond. What can I do? Can I force these residues to form S-S bond in
> .gro file?
>

Make a copy of specbond.dat in the working directory and adjust the reference 
distance for the disulfide.  pdb2gmx should print out the distance matrix, so 
you know how far the atoms are to make the proper adjustment.

http://www.gromacs.org/Documentation/File_Formats/specbond.dat

-Justin

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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
http://mackerell.umaryland.edu/~jalemkul

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