[gmx-users] C-terminal amidation of peptide

[anna Kalkbrenner]

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?

Best regards,

Anna
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