Please patch the pbsa related bugfixes in Amber8 and run again.
Ray
Xioling Chuang wrote:
> Dear All,
>
> I have used mm_pbsa to extract 1000 snapshots of complex (DNA duplex),
> receptor (1st strand), and ligand (2nd strand). When mm_pbsa
> calculated PB upto snapshot 359, pbsa output stopped with message
> ---File "pbsa_com.359.out" ---
> .
> .
> .
> Iteration data
> Maximum iterations : 500
> Convergence criteria: 1.000000000000000E-003
> Iterations required : 12
> Norm of the constant vector: 7829.90318844151
> Norm of the residual vector: 4.66126368647964
> Convergence achieved : 5.953156219556570E-004
>
> PB Bomb in epsbnd(): No neighbor found for exposed boundary
> grid 51
> 79 32
> ----------------------------
>
> 1. Is this problem caused by bad geometry of complex? I have visualed
> the molecule and it looked fine.
> 2. What should I solve the problem to complete the pbsa calculation of
> all snapshots?
> 3. If this is a problem of a bad geometry of snapshot, how mm_pbsa.pl
> ignores such snapshot and continue the next snapshots in order to
> complete the calculation?
>
> Thank you very much in advance.
>
> Best Regards,
> Xioling
>
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--
====================================================
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.uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
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Received on Tue Nov 29 2005 - 18:53:01 PST
