Hi,
Sorry, but I am still facing problems with mm-pbsa. I increased cutres to 15
but then I had another error with memory, which I solved recompiling pbsa in
single precision (as suggested in amber list). Now I am having the following
error:
-- > MAXAT=10000 exceeded
molsurf: molsurf.c:1055: is_buried: Assertion `sarg1 >= 0.0' failed.
Use of uninitialized value in multiplication (*) at
/scratch/amber8/src/mm_pbsa/mm_pbsa_statistics.pm line 1336.
Use of uninitialized value in multiplication (*) at
/scratch/amber8/src/mm_pbsa/mm_pbsa_statistics.pm line 1336.
Use of uninitialized value in multiplication (*) at
/scratch/amber8/src/mm_pbsa/mm_pbsa_statistics.pm line 1336.
No data for 0+0 MS SURF 0
[1] Exit 134 mm_pbsa.pl mm.exp.in > mm.exp.out
The statistics.in is produced but not the statistics.out. Since I previously
increased the MAXAT variable, I really donīt know why it is giving problems
now. Do you (or anyone else) have any suggestion about how to solve this? Is
it possible that something is wrong with my input files? I am sending you my
pdb for the whole complex (created by ambpdb), in and charge files as
attachment.
Best regards
Miguel
>From: "Ray Luo" <rluo.uci.edu>
>Reply-To: amber.scripps.edu
>To: amber.scripps.edu
>Subject: Re: AMBER: MM-PBSA problem
>Date: Fri, 14 Apr 2006 14:40:45 -0700
>
>
>>I set radiopt=0 and now I am getting the error message in the output file
>>as: PB bomb in pb_reslist(): maxnbr too small.
>
>As have been discussed on the mailing list before, please use a longer
>cutres to get rid of this error message.
>
>--
>====================================================
>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 Apr 18 2006 - 03:02:42 PDT
