AMBER Archive (2004)

Subject: Re: AMBER: leap.log warnings

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Sun Jun 20 2004 - 21:52:17 CDT

> When I build topology and coordinate files using leap, it looks fine--
> just give out a list of 'old PREP-specified impropers'. But I find the
> leap.log shows many warnings like:
> -------
> ** Warning: No sp2 improper torsion term for CY-HC-CX-HC
> atoms are: CAB HVC2 CBB HVT2
> -------
>
> What does it mean? Could it has influence on MD? Any help would be
> highly appreciated!
 
If you loaded a prep.in file for that residue and that file
has an IMPROPER section, this message probably means that
an improper in the prep.in was not matched by a parameter and
so no improper torsion was added to the prmtop.

This means that loading the prep file of a new residue and saving
a prmtop can help determine if the ff parmeters are there for all
the improper torsions you desire. This is a little-known feature
that was used for development of the then-new leap improper torsion
assignment algorithm.

In any case, you should consider whether there should be an improper
torsion around atom CBB. If so, you would need to add one via loading
a frcmod file before saveamberparm.

Bill
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