AMBER Archive (2002)

Subject: Re: mm_pbsa

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Sun Sep 22 2002 - 16:01:22 CDT

Sue Heavner wrote:
>
> Hi:
> I am using mm_pbsa in amber7. I would like to include Na ions in the
> calculations but keep getting errors including "bad atom type: IP"
> and
> "Can't use an undefined value as an ARRAY reference at
> /usr/local/amber7/src/mm_pbsa/mm_pbsa_statistics.pm line 1234.". I
> think maybe I need to modify the code in mdread.f. Can anybody help?
>
> Thank-you, Sue Heavner

Dear Sue,

the "bad atom type" message indeed comes from the parameter assignment
for SA calculations within mdread.f (and the "... undefined value ..."
is a follow up then). You might have a look at the section for Mg ions
there as a starting point to extend the code for your purposes.

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
+++++++++++++++++++++++++++++++++++++++++++++