[gmx-users] C-terminal amidation of peptide

Justin A. Lemkul jalemkul at vt.edu
Sun Mar 20 05:12:03 CET 2011

anna Kalkbrenner wrote:
> Hello,
> 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?

Your approach is correct.  Use your favorite editing software to add the 
appropriate group.  There are some useful programs listed on the Gromacs site, 
but unfortunately it is currently down.  xLeap is a pretty useful tool, although 
there are many others that can accomplish the same; for simple amide addition 
you could probably add it manually with a bit of geometry :)


> Best regards,
> Anna


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


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