[gmx-users] Using specbond.dat in pdb2gmx

Matthew Stancea mstancea at ggc.edu
Tue Jun 17 22:44:10 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!


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...

-Matthew Stancea

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