[gmx-users] breaking S-S bond using pdb2gmx

Justin Lemkul jalemkul at vt.edu
Mon Feb 16 13:40:14 CET 2015

On 2/16/15 4:27 AM, Sahithya S Iyer wrote:
> Deal all,
> I need to break 1 out of 4 S-S bonds in a protein. While using the pdb2gmx
> command, i used -ss whereby i was asked which S-S bonds i would what to
> keep intact and which i'd break. Since i wanted the S-S bond between CYS
> 6-CYS 127 to be broken, i gave he following command -
> Link CYS-6 SG-48 and CYS-127 SG-981 (y/n) ?n
> Link CYS-30 SG-238 and CYS-115 SG-889 (y/n) ?y
> Link CYS-64 SG-513 and CYS-80 SG-630 (y/n) ?y
> Link CYS-76 SG-601 and CYS-94 SG-724 (y/n) ?y
> The .gro file generated , visualised using vmd, shows 4 S-S bonds instead
> of 3. Where have i gone wrong. Is there any other method the break the S-S
> bonds present in the pdb file ?

The topology is definitive, not what you see in VMD.  Though the -SH groups 
should be obviously present.  Make sure you're visualizing the right file.



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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