AMBER Archive (2004)

Subject: Re: AMBER: leap.log warnings

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Mon Jun 21 2004 - 12:40:13 CDT

> > 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".

That is exactly what I am trying to say. :-)

> 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).

Leap should silently ignore these UNLESS it has loaded a prep.in
for the residue that has an IMPROPER section, in which case it would
warn the user when the ff did not cover that explicit improper. I added
this feature for debugging when amber/leap switched from using
the IMPROPER section to assigning only ff-defined impropers.

It is too confusing to print a warning for every potential improper
that does not have a ff term.

Bill
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