Thanks!
On Fri, Dec 16, 2011 at 9:22 PM, case <case.biomaps.rutgers.edu> wrote:
> 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
>
>
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--
Chris Bryant
Biochemistry B.S.
Philosophy B.A.
Vice President, Alpha Chi Sigma
Case Western Reserve University 2013
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Received on Sat Dec 17 2011 - 08:00:03 PST
