AMBER Archive (2004)

Subject: AMBER: PB bomb in pb_saarc

From: S. Frank Yan (SYan_at_gnf.org)
Date: Tue May 18 2004 - 15:41:41 CDT


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

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?

Thanks a lot,
Frank

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