[gmx-users] problems with Cysteines

Justin Lemkul jalemkul at vt.edu
Fri Jan 17 22:04:18 CET 2014

On 1/17/14, 2:48 PM, Steve wrote:
> I have attempt to make present in my confout.gro structure both CYSH and CYS.
> I was able to do so, but only by modifying the FF (renaming CYS to CYX in
> both my pdb file and the forcefield used). If I took out the HG hydrogen in
> pdb and left the name as CYS in forcefield, pdb2gmx would add a HG atom to
> confout.gro automatically.
> According to what I have read in manual and on-line is that if I do the
> following:
> $pdb2gmx -f name.pdb -ss -his
> I should be able to select what cysteines and histidines I what protoned
> etc....
> HOWEVER, when I do this the code pdb2gmx lets me select His, but does not
> allow any changes to Cys (to make s-s bonds or anything). Am I doing
> something wrong here?
> Could someone please tell me what I can do to make a S-S bond...do I have to
> use "specbond.dat"???

You don't have to manually use specbond.dat, because pdb2gmx always reads it. 
When using -ss, pdb2gmx detects Cys residues that are within an appropriate 
distance to form a disulfide, then asks you if you want those Cys residues to be 
free or involved in that disulfide.  If you are not being given any such option, 
that means none of the S-S distances are within suitable range of a typical 
disulfide bond.  In specbond.dat, the distance is set to 0.2 nm, and the default 
tolerance (hard coded) is 10%, so if the S-S distance is less than 0.18 or more 
than 0.22, no disulfide is detected and no prompt is produced.  If you believe 
your structure should have disulfides that occur at some other distance, then 
you can make a copy of specbond.dat in your working directory and alter the 
default distance as you like.



Justin A. Lemkul, Ph.D.
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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