AMBER: mm_pbsa example

From: Jory Zmuda <>
Date: Thu, 09 Oct 2003 16:35:21 -0400


I am trying to run the Stability example for MM_PBSA. Whenever I run
the script, I have numerous lines stating various "Illegal character in
prototype for mm_pbsa_statistics:..."

My input parameters are then read in and then it starts running:

=>> Checking sanity
     Checking GENERAL
     Checking MM
     Checking DELPHI
     Checking GB
     Checking MS

=>> Creating input
     Sander input
     Delphi input

=>> Calculating energy / entropy contributions

=>> Doing statistics
=>> Values of global variables
     TEMP = 300
     R = 8.314
     gammaP = 0.00542
     betaP = 0.092
     gammaG = 0.0072
     betaG = 0.00
=>> Reading input
=>> Reordering files
     Final order:
     1. ras_raf_II_wt_com.all.out: -
=>> Reading files
     Reading ras_raf_II_wt_com.all.out
=>> Treat special parameters
Can't use an undefined value as an ARRAY reference at
/usr/local/amber7/src/mm_pbsa/ line 1234.

The program then quits and the output does not have any of the energies.
  I saw on the archive that this happens when certain ions are not
parameterized, and I see that there is a Mg ion in the prmtop file. Why
would the example not work?

Thank you,
Jory Zmuda

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Received on Thu Oct 09 2003 - 21:53:01 PDT
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