[gmx-users] C-terminal amidation of peptide

Mark Abraham mark.abraham at anu.edu.au
Sun Mar 20 05:24:02 CET 2011

On 20/03/11, anna Kalkbrenner  <anna.kalkbrenner at gmail.com> 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?

Correct treatment of termini differs widely with the forcefield. Some forcefields have special residue types that contain just the terminal atoms, some force fields have special residue types and include the whole residue preceding the terminal atoms and the terminal atoms. You will need to look in the residuetypes.rtp file for the forcefield you have in mind and see what possibilities are already supported.

pdb2gmx -ter and "none" merely directs pdb2gmx not to change anything using the terminus databases (.tdb), however what is in your input coordinate file (and now unmodified) still has to be supported by the .rtp. More details in chapter 5 of the manual, of course.

>   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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