AMBER Archive (2003)

Subject: Re: question about mm_pbsa?

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Tue Mar 18 2003 - 15:05:29 CST

Hi,

this was a bug in sander - surface area routines did not know about gaff
atom types. This can be corrected by applying bugfix.7.
(http://www.amber.ucsf.edu/amber/bugfixes/7.0/bugfix.7)

Best regards

Holger

> Hi:
> I changed IGB=1, then I get new error:
>
> bad atom type: c3
>
> c3 is atom type used in gaff force field. But the program can not identify
> it. It's kind of strange.
>
> Lishan
>
> >
> > Hi,
> >
> > as it says in the manual, the IDECOMP variable in sander is meant to be
> > set by the mm_pbsa script (if DC=1 and according to DCTYPE in the
> > @DECOMP section in mm_pbsa.in). The error message below occurs because
> > decomposition only works in the case of GB models (i.e. IGB must be > 0
> > in sander.in).
> >
> > Best regards
> >
> > Holger
> >
> > > I try to decompose the energies for my MD result by using mm_pbsa. But
> it
>
> > > stops, and I get this information from the sander output.
> > >
> > > IDECOMP is not compatible with EWALD 

-- 
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
email: gohlke_at_scripps.edu
+++++++++++++++++++++++++++++++++++++++++++++