AMBER Archive (2004)

Subject: Re: AMBER: PB bomb in pb_saarc

From: Ray Luo (rluo_at_uci.edu)
Date: Mon May 17 2004 - 17:58:21 CDT

S. Frank Yan wrote:

>Hi,
>
>I was trying to use the pbsa program to compute the salvation free
>energy of a protein-ligand complex. The pbsa.in input is generated from
>mm_pbsa.pl with radiopt set to 0, and the error message is:
>
>Number of SA srf points exposed 53573
> PB bomb in pb_saarc(): Allocation aborted 0
> 494 494
>
This indicates that your computer does not have enough memory to
allocate the arrays for calculation of solvent accessible arcs.You can
try a larger grid spacing to see whether this still happens.

>
>Also, a related question on setting the radius parameters of the ligand
>in pbsa which does not recognize the small-lettered atom types generated
>from GAFF. Is it possible that we can use the PARSE parameters?
>

This is possible only with radiopt=0, i.e. radii read in from the prmtop file. You'll have to write a script to put the parse radii into the radius section of your prmtop file. We thought about putting parse radii in pbsa before amber8 was released. We eventually gave up the idea since amber charges are not very compatible with parse radii. 

-- 
====================================================
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: rluo_at_uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
====================================================

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu