AMBER Archive (2003)

Subject: Re: mm_pbsa error message

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Sun Jun 08 2003 - 11:19:24 CDT

chernhoe wrote:
>
> I got the following error message while running mm_pbsa. It worked for a
> non-periodic case, but in this case, the protein is solvated in water,
> and mm_pbsa gave the following message. I will email the necessary files
> to anyone willing to help. Thanks.
>
> --------------------------------------------------------------------------------
> 3. ATOMIC COORDINATES AND VELOCITIES
> --------------------------------------------------------------------------------
>
>
> FATAL: NATOM mismatch in coord and topology files

I assume that you have stripped water molecules and counter ions from
the trajectory while generating the snapshots for mm_pbsa. Thus, for
calculating energies, you need to provide a prmtop file which doesn't
contain water molecules and counter ions either (i.e. repeat the
generation of the prmtop file but don't "solvate..." and don't
"addIons"). Otherwise, the number of atoms (NATOM) do not agree - as
indicated above.

Best regards

Holger 

-- 
+++++++++++++++++++++++++++++++++++++++++++++
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
+++++++++++++++++++++++++++++++++++++++++++++