On Thu, May 31, 2012, Thorsten Pisternick wrote:
>
> > I have calculated the zwitterionic peptides using the ff99SB
> > forcefield, but now i have problems loading the *.pdb data with the
> > protonated peptide into leap.
The residue and atom names in the input pdb file must exactly match those
in the library files you are using. Amber doesn't provide library files
for a protonated C-terminal residues, so you will have to construct them
yourself. This is by no means a trivial task, and you might want to consider
whether having an NH2 or NH(CH3) capping group might serve your needs.
If you indeed need a protonated C-terminal residue, see the tutorials for
ideas on getting started in defining new residue types. The R.E.D. website
might also help.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 31 2012 - 04:30:03 PDT
