[gmx-users] Using specbond.dat in pdb2gmx

Justin Lemkul jalemkul at vt.edu
Wed Jun 18 22:41:51 CEST 2014

On 6/18/14, 3:31 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
> My apologies! My description was not very clear, and now I see that. However, because you mentioned that HG would be the name of the hydrogen attached to the sulfur, I believe that perhaps changing the name of some of the hydrogens in the pdb file can fix the issue.
> After editing the pdb only in the area of the names of the atoms (such as HB3), I was able to generate a topol.top file with a bond between the first nitrogen and the last carbon. However, I still have 2 too many hydrogens on the first nitrogen and 1 too many oxygens on the last carbon.

You need to be using -ter and choosing "None" for both termini, otherwise the 
default behavior takes over and pdb2gmx builds ionized termini.  You don't have 
free termini, so you have to take control of pdb2gmx.



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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