On Sun, Jun 9, 2013 at 2:23 AM, BERGY <nucleic81.gmail.com> wrote:
> Dear All,
> I am unable to do Alanine scan for the terminal residues of my peptides.
> Could it be that the terminal residues cannot be used correctly in MMPBSA
> since they might contain OXT and NH3 atoms in the atom number does not
> match.
>
> I saw that a similar question was asked
> http://archive.ambermd.org/201303/0372.html and with no reply.
>
I remember adding support for terminal residues (or trying to, at least),
but that case has not been exhaustively tested for sure. Can you send me
the input files along with a sample trajectory that has 1 or 2 frames
present so I can try to debug?
Thanks,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 10 2013 - 20:30:04 PDT
