Vikas,
The error message is due to lack of memory on your computer. First set
fillratio = 2 for proteins, and if the error message persists, increase
space to 0.75, 1.00, and so on.
Ray
==========================================
Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email: rluo.uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================
Vikas Sharma wrote:
> Dear Dr. Ray Luo,
>
> Sorry for replying so late...actualyy i checked the output file, found an erro..rectified it and re-ran the command:
>
> mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log
>
>
> i got the follwing error:
>
> /opt/amber10/exe/sander -O -i pbsa_com.in -o pb sa_com.7.out -c /home/bharatam/amberresults_w/amberresults31/snapshot_com.crd.7 -p /home/bha ratam/amberresults_w/amb31/A31.prmtop not successful
>
>
> the contents of the output file are pasted below:
>
> ======== Setting up Grid Parameters ========
> Using bounding box for grid setup
> Bounding Box Center: 47.000 43.500 29.000
> Xmin, Xmax, Xmax-Xmin: -6.933 100.641 107.574
> Ymin, Ymax, Ymax-Ymin: -18.558 105.341 123.899
> Zmin, Zmax, Zmax-Zmin: -29.798 88.266 118.064
> beginning box center at level 1 47.000 43.500 29.000
> beginning box center at level 2 47.000 43.500 29.000
> Grid dimension at level 1 109 125 119
> Grid origin corrected at level 1 -173.000 -208.500 -211.000
> Grid dimension at level 2 229 263 251
> Grid origin corrected at level 2 -10.500 -22.500 -34.000
> SA surface: setting up working radii
> SA surface: found nonzero radii 3777
> Number of SA srf points exposed455488
> SA Bomb in sa_arc(): Allocation aborted 0 0 41
> 0 0
>
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Received on Sun Jun 07 2009 - 01:08:26 PDT
