[gmx-users] C-terminal amidation of peptide
ljggmx at yahoo.com.sg
Sun Mar 20 09:04:27 CET 2011
If you use CHARMM FF and Gromacs4.5 or later, you can use -ter in pdb2gmx and
choose CT2 to add NH2 at C-terminus. For other FF, you may need to manually add
NH2 in pdb file.
From: anna Kalkbrenner <anna.kalkbrenner at gmail.com>
To: gmx-users at gromacs.org
Sent: Sunday, 20 March 2011 11:59:34
Subject: [gmx-users] C-terminal amidation of peptide
I'm sorry if my questions are on the elementary level, as I am still learning
how to use GROMACS. I would like perform an MD run on a peptide that has an
amidated c-terminal. My understanding is that I can modify my PDB structure to
include the NH2 group. Then, with pdb2gmx I use the "-ter" option and select
"none" for the C-terminus. Is this correct? What is the best way to edit the
PDB file to add the amide group? Can it be done through a structural editor?
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