[gmx-users] puzzling about adding H atoms

Justin A. Lemkul jalemkul at vt.edu
Sat Jul 4 03:23:58 CEST 2009

wuxiao wrote:
> Dear gmx users, Through the manual, I learn of that both pdb2gmx and
> protonate can add H atoms according to the hdb files.  About it, I have some
> puzzles as follows: Are the two programs equivalent in adding H atoms? If it
> is yes, why bother to develop another program? It seems that protonate
> program can not generate partial atom charges, so after protonation, it still
> needs to do so.

Using pdb2gmx will add only the H atoms specified by the force field - for UA
force fields this is polar H atoms only.  Using protonate will add all H atoms
according to valence requirements of all atoms (i.e., a CH2 group would get 2 H
atoms, while in a UA force field, no H atoms would be present).


> Thanks a lot ahead for any reply.
> Best regards Chaofu Wu
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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