On Fri, Dec 16, 2011, Chris Bryant wrote:
>
> I am working with a protein with an inhibitor attached to the oxygen of a
> serine and I am wondering what the naming convention is for tleap. If it
> helps, the part of the inhibitor it is attached to is a carbon. If I need
> to provide more information please tell me.
There is no naming convention. You probably want to create a modified
residue = serine + modification (assuming this is a covalent modification).
You can call that residue whatever 3-letter name you want; you just need
to use the same residue and atom names in the PDB file as in the library
file you create.
(See the antechamber module or the R.E.D. website,
http://q4md-forcefieldtools.org/, for instructions on creating amber libraries
for modified amino acids.)
...good luck....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Dec 16 2011 - 18:30:02 PST
