[gmx-users] more than one protonation per residue with pdb2gmx

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 12 12:08:14 CEST 2012

On 7/12/12 4:37 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> I have another question about the option -ter of the pdb2gmx command.
> I choose it because I thought that this is a way that I can determine what
> shell happen with the termini but I was not ask anything by the program.
> My aim is it to block the termini with a neutral group. Is there a way to
> do this with gromacs?

Yes.  You need to build the appropriate groups onto your protein's structure 
using normal capping groups present within the force field (ACE, NME, NH2, etc) 
and choose "None" for the termini when running pdb2gmx so that no additional 
protons are added or removed; the first and last amino acids are then treated as 
internal residues with normal peptide bonds.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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