[gmx-users] How to change the protonation state of an aminoacid in a peptide

Camilo Andrés Jimenez Cruz camilo.jimenezc at gmail.com
Wed Jul 29 22:43:30 CEST 2009


I have the gro file for a peptide in vacuum, in the peptide, there is
only one ASP, and I want to change it to ASPH.
If I run pdb2gmx -asp and select the protonated state, the only change
is in the name of the residue (it doesn't add the needed hydrogen).
Is there any automatic way changing the protonated state for this residue?

Thanks in advance
Camilo Andrés Jiménez Cruz

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