Re: mm_pbsa

From: Holger Gohlke <>
Date: Sun 22 Sep 2002 14:01:22 -0700

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/ 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


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
Received on Sun Sep 22 2002 - 14:01:22 PDT
Custom Search