AMBER Archive (2004)

Subject: Re: AMBER: phosphoserine library component

From: David A. Case (case_at_scripps.edu)
Date: Fri Sep 24 2004 - 10:25:10 CDT

On Fri, Sep 24, 2004, jwcraft_at_uh.edu wrote:
>
> I have been foiled in my attempt to build a phosphoserine library for
> AMBER despite the fact that I know that others seem to have done it.
>
> 1) Build the residue in Insight, used its optimization to relax the
> molecule to get appropriate bond angles, and lengths
> 2) Run antechamber to get a sep.prepin library fragment to use in tleap

> For atom: .R<SEP 9>.A<O2P 1> Could not find type: o
> For atom: .R<SEP 9>.A<P 2> Could not find type: p5

By default, antechamber uses the GAFF atoms types, which are all lower case.
You will have to load gaff.dat to get access to these.

However, antechamber is not well set up to build amino acid residues; it was
designed only for complete molecules. You are probably better off starting
with SER and converting that to PSER using xleap, and using the upper case
atom types. You will then have some missing parameters, and can use the
suggestions from GAFF to create a frcmod file that has some of the missing
parameters.

As I have mentioned here before, I keep hoping that some friendly "kinase"
person will contribute some PSER, PTHR files to the contributed parameters
database....

...dac

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