[gmx-users] disulfate bond between 2 chains

Justin Lemkul jalemkul at vt.edu
Wed Apr 20 11:46:40 CEST 2016

On 4/20/16 5:20 AM, Ming Tang wrote:
> Dear list,
> Is there anybody who generated the disulfate bonds between 2 different chains? I used -chainsep but did not get what I want. If I choose -chainsep interactive (n), it will generate the disulfate bond between 2 chains (only after enlarge the bond distance in specbond.dat), but I just came across one C and one N-terminal option, which is not correct. It seems that pdb2gmx use this disulfate bond to connect 2 chains into one.

You want -merge, not -chainsep.



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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