AMBER Archive (2009)

Subject: [AMBER] ANAL problems

From: E.M. (
Date: Tue Apr 28 2009 - 15:12:04 CDT

Hello, I wanted to go ANAL ;-) to do a decomposition of the
energies in a snapshot but got this:

 Max Nonbonded Pairs: 82805 packed 1 to a machine word
   3. A T O M I C C O O R D I N A T E S


          NUMBER OF ATOMS = 56897

          loading the groups for analysis

    ----- END OF GROUP READ -----

    non-bonded pairs are generated in residue base
    and stored as residue pairs

  Number of NB Res pairs =******** exceeds max = 82805
My question is how to change the Max Nonbonded Pairs?
I found this variable is not defined in the anal directory
where is this localted?. How to change it?

Is it possible to run first ptraj to get rid of the waters
and then perhaps run anal in the ptraj output or that format is not



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