AMBER Archive (2004)

Subject: Re: AMBER: PB bomb in pb_saarc

From: Ray Luo (
Date: Tue May 18 2004 - 19:54:21 CDT

S. Frank Yan wrote:

>Thanks for the reply. It's unlikely that the machine didn't have enough
>physical memory, since the particular machine I was working on has over
>3G total and at least 1G free when I ran the program. Also, if I were
>to use the radiopt=1 option, is there any way I could circumvent the
>inconsistency between pbsa and gaff, say by modifying the pbsa code to
>recognize small letter, or visa verse?
Hi Frank,

Could you email me (_not_ to the list) your prmtop, rst, and input files
so that I can take a look of the problem?

For the question on radii, pbsa has a default radii assignment rule for
radiopt=1 (in routine "pb_aaradi" of file "pb_init.f"). If you can
change the code to ignore upper-case/lower-case in atom types, you
should be able to use that default rule. We didn't make the radii
assignment very comprehensive because these should really go to leap in
the future.


Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
Fax: (949)824-8551          e-mail:
Home page:

----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to