[gmx-users] Using specbond.dat in pdb2gmx

Justin Lemkul jalemkul at vt.edu
Tue Jun 17 22:50:30 CEST 2014

On 6/17/14, 4:43 PM, Matthew Stancea wrote:
>> Or observe that the .rtp entry has names like HB1 and HB2, rather than HB2
> and HB3 and use sed (or your text editor) to do the replacement.
>> ie. do the replacement on your input coordinate file, not the .rtp!
>> Mark
> Dr. Mark Abraham,
> My pdb file contains HB1 and HB2 on a beta carbon of a cysteine. Well, connected to that carbon (other than the alpha carbon) is the sulfur molecule. The only logical placement of for "HB3" is to that sulfur, except that the sulfur should not have any hydrogens bound to it since it is supposed form a disulfide bridge with another cysteine.
> Because of that, I am sure you can understand why I am scratching my head on this issue...

HB3 is sometimes the nomenclature of beta carbons (some programs write HB2 and 
HB3 instead of HB1 and HB2, and the B means "beta").  Your description doesn't 
make any real sense to me.  Visualize your structure.  If you have a full set of 
protons on Cys, you should have HA, HB1, and HB2 on the side chain to make the 
force field happy.  If there is an HG on SG (the sulfur atom), then it will be 
deleted by pdb2gmx when you tell it to create a disulfide.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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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