AMBER Archive (2004)

Subject: Re: AMBER: leap.log warnings

From: David A. Case (case_at_scripps.edu)
Date: Mon Jun 21 2004 - 10:43:07 CDT

On Sun, Jun 20, 2004, Bill Ross wrote:

> > 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.

Bill may be correct here, but my reading of the code is that LEaP prints
but otherwise ignores any "PREP-specified impropers". I believe that this
warning is coming from an improper that leap is trying to create by its
algorithm for deciding where impropers might be needed (that is, around atoms
bonded to exactly three other atoms).

> 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.

The above is correct. Your atom names don't seem to come from the standard
Amber protein and nucleic force fields, so you will have to decide whether
there should be such an improper torsion or not. If not, then you should just
ignore the warning.

...hope this helps...dac

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