[gmx-users] Using specbond.dat in pdb2gmx

Matthew Stancea mstancea at ggc.edu
Wed Jun 18 21:31:18 CEST 2014

>>> 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.


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. 

However, even with this small discrepancy, I am astounded that I was able to finally generate a conf.gro and topol.top of a cyclotide with a bond between the terminal N and the terminal C!

Thank you so much for your help, Dr. Lemkul and Dr. Abraham!


-Matthew Stancea

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