[gmx-users] C-terminal amidation of peptide

Jianguo Li 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?

Best regards,


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