[gmx-users] Is there a way to add protons to all the residues in a given system?

Justin A. Lemkul jalemkul at vt.edu
Tue Dec 9 02:36:45 CET 2008

Arthur Roberts wrote:
> Hi, all,
> This is probably an obvious question.  I did a simulation with an ff53a6 
> force field, which lacks protons on aliphatic side chains.  I have pdb 
> coordinates for each time.  Is there a way to add protons to the 
> aliphatic side chains.  Your input is appreciated.

Check out the "protonate" tool.


> Sincerely,
> Art Roberts
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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