[gmx-users] C-terminal amidation of peptide
anna.kalkbrenner at gmail.com
Sun Mar 20 04:59:34 CET 2011
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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