AMBER Archive (2006)

Subject: AMBER: problems on mm_pbsa

From: Giovanni (giovanni.grazioso_at_unimi.it)
Date: Wed Jun 14 2006 - 07:05:03 CDT

Dear all,
        when I run Amber9/mm_pbsa, it gives me "MAXAT=10000 exceeded" .
As has been reporteb on the Amber Mailing list Archive (e-mail Apr 29
2004), I modified the molsurf.h file on the $AMBERHOME/src/mm_pbsa
directory and then, compiling all, I obtained the same error.
Mm_pbsa module works well with the ligand but when I use the receptor or
the complex (17000 atoms) other errors like this occurred:

        Use of uninitialized value in multiplication (*)
        at /home/gianni/programmi/amber
        9/src/mm_pbsa/mm_pbsa_statistics.pm line 1376.
        Use of uninitialized value in multiplication (*)
        at /home/gianni/programmi/amber
        9/src/mm_pbsa/mm_pbsa_statistics.pm line 1376.
        Use of uninitialized value in multiplication (*)
        at /home/gianni/programmi/amber
        9/src/mm_pbsa/mm_pbsa_statistics.pm line 1344.
        Use of uninitialized value in multiplication (*)
        at /home/gianni/programmi/amber
        9/src/mm_pbsa/mm_pbsa_statistics.pm line 1344.
        Use of uninitialized value in multiplication (*)
        at /home/gianni/programmi/amber
        9/src/mm_pbsa/mm_pbsa_statistics.pm line 1475.
        Use of uninitialized value in multiplication (*)
        at /home/gianni/programmi/amber
        9/src/mm_pbsa/mm_pbsa_statistics.pm line 1475.
        No skew or curtosis when zero variance in moment
        No skew or curtosis when zero variance in moment
        Use of uninitialized value in addition (+)
        at /home/gianni/programmi/amber9/src/
        mm_pbsa/mm_pbsa_statistics.pm line 1761.
        Use of uninitialized value in addition (+)
        at /home/gianni/programmi/amber9/src/
        mm_pbsa/mm_pbsa_statistics.pm line 1761.
        Use of uninitialized value in subtraction (-)
        at /home/gianni/programmi/amber9/s
        rc/mm_pbsa/mm_pbsa_statistics.pm line 1773.
        Use of uninitialized value in subtraction (-)
        at /home/gianni/programmi/amber9/s
        rc/mm_pbsa/mm_pbsa_statistics.pm line 1773.
        No skew or curtosis when zero variance in moment
        Use of uninitialized value in addition (+)
        at /home/gianni/programmi/amber9/src/
        mm_pbsa/mm_pbsa_statistics.pm line 1761.
        Use of uninitialized value in addition (+)
        at /home/gianni/programmi/amber9/src/
        mm_pbsa/mm_pbsa_statistics.pm line 1761.
        Use of uninitialized value in subtraction (-)
        at /home/gianni/programmi/amber9/s
        rc/mm_pbsa/mm_pbsa_statistics.pm line 1773.
        Use of uninitialized value in subtraction (-)
        at /home/gianni/programmi/amber9/s
        rc/mm_pbsa/mm_pbsa_statistics.pm line 1773.
        No skew or curtosis when zero variance in moment
        Use of uninitialized value in addition (+)
        at /home/gianni/programmi/amber9/src/
        mm_pbsa/mm_pbsa_statistics.pm line 1761.
        Use of uninitialized value in addition (+)
        at /home/gianni/programmi/amber9/src/
        mm_pbsa/mm_pbsa_statistics.pm line 1761.
        Use of uninitialized value in subtraction (-)
        at /home/gianni/programmi/amber9/s
        rc/mm_pbsa/mm_pbsa_statistics.pm line 1773.
        Use of uninitialized value in subtraction (-)
        at /home/gianni/programmi/amber9/s
        rc/mm_pbsa/mm_pbsa_statistics.pm line 1773.
        No skew or curtosis when zero variance in moment

Another problem occurred on tleap when I tried to source leaprc.ff02,
the programs doesn't find the file.

Any adivce will be appreciated, thanks in advance!

Giovanni Grazioso

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