AMBER Archive (2006)

Subject: AMBER: amber9: SA Bomb in sa_arc

From: Giulio Rastelli (rastelli.giulio_at_unimo.it)
Date: Wed Oct 25 2006 - 06:03:54 CDT

Dear developers,
I am using amber9 to run mm_pbsa calculation on a protein-ligand complex.
Using a SCALE parameter of 2 (grid space 0.5), PBSA works fine.
When I try to increase the SCALE parameter to 4 (grid space 0.25)
I have this error:
   SA surface: setting up working radii
   SA surface: found nonzero radii 5172
  Number of SA srf points exposed 52227
  SA Bomb in sa_arc(): Allocation aborted 0 0
        1 0 0

I am using a fillratio equal to 4.
Looking at the amber9 code is_init.f, it seems to me that the maxarc
and/or maxarcdot have to be redimensioned to higher values.
Before doing that, I would prefer receiving a feedback from
the developers.
Thank you very much in advance
Giulio

part of MM_PBSA input:
______________________________
@PB
PROC 2
REFE 0
INDI 1.0
EXDI 80.0
SCALE 4
LINIT 1000
PRBRAD 1.4
#
RADIOPT 0
NPOPT 1
CAVITY_SURFTEN 0.0072
CAVITY_OFFSET 0.00
______________________________ 

-- 

Prof. Giulio Rastelli
Dipartimento di Scienze Farmaceutiche
Facolta' di Bioscienze e Biotecnologie
Universita' di Modena e Reggio Emilia
Via Campi 183
41100 Modena - ITALY
-------------------------------------
tel 0039-059-2055145
fax 0039-059-2055131
www.scifar.unimore.it/on-line/Home/Gruppidiricerca/Prof.GiulioRastelli.html
-------------------------------------

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