AMBER Archive (2006)

Subject: AMBER: MM_PBSA error

From: Shozeb Haider (shozeb.haider_at_pharmacy.ac.uk)
Date: Tue Oct 03 2006 - 16:04:57 CDT

Hi,

I am trying to run mm_pbsa. My system is a DNA molecules with K+ ions.

I dont get any problems while creating coordinates however when I run
the stability script it always gives me the error message

Use of uninitialized value in multiplication (*) at
/usr/local/amber9/src/mm_pbsa/mm_pbsa_statistics.pm line 1472.
Use of uninitialized value in multiplication (*) at
/usr/local/amber9/src/mm_pbsa/mm_pbsa_statistics.pm line 1472.
    No data for 0+0 MM VDWNB 0

I have looked into the mm_pbsa_stability.out file and the only warnings
I have are

=>> Reading files
    Reading b19_com.all.out
    WARNING: Missing VDWNB for MM in 0 -> Taken from -1
    Reading b19_rec.all.out
    Checking CALC
    WARNING: Missing VDWNB for MM in 0 -> Taken from -1
    Reading b19_lig.all.out
    Checking CALC

I should also mention that I have added K+ in
/usr/local/amber9/src/mm_pbsa/mm_pbsa_calceneent.pm

Can any one point me in the right direction as to what I might be doing
wrong ?

Many thanks

Shozeb

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