AMBER Archive (2005)

Subject: Re: AMBER: doubts with a new aminoacid

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue Feb 01 2005 - 18:36:38 CST

> > LOOP
> > CG CD2
> > CE2 CD2
>
> You need a blank line between the LOOP section and the IMPROPER section
> (that is, right here).
>
> > IMPROPER
> > -M CA N H
> > CA +M C O
> > CD1 CE2 NE1 HE1
> > CE2 CH2 CZ2 OZ2
> > CZ2 CZ3 CH2 NH2
> > CH2 CE3 CZ3 HZ3
> > CG NE1 CD1 HD1
> > CD1 CD2 CG CB
> > DONE
> > STOP
>
> However, LEaP ignores any improper torsions specified in the prep files.
> You should use rdparm to examine a prmtop file that contains this new residue,
> to make sure that you are getting the terms you want.

If you load the prep file directly (instead of a lib file),
leap will (used to anyway) keep track of the impropers from
the IMPROPER section, and check whether the ones the ff
generates correspond. I added this feature when validating
leap's handling of the ff's.

Bill
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