AMBER Archive (2004)

Subject: RE: AMBER: PB bomb in pb_saarc

From: S. Frank Yan (SYan_at_gnf.org)
Date: Tue May 18 2004 - 18:14:36 CDT

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?

Frank

> -----Original Message-----
> From: Ray Luo [mailto:rluo_at_uci.edu]
> Sent: Monday, May 17, 2004 3:58 PM
> To: amber_at_scripps.edu
> Subject: Re: AMBER: PB bomb in pb_saarc
>
> 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/
> ====================================================
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