[AMBER] Non-polar solvation free energy in AMBER11 MMPBSA.py

From: Tong Zhu <tongzhu9110.gmail.com>
Date: Thu, 11 Oct 2012 14:55:07 +0800

Dear everyone,

Thank you very much for your time. I have a protein-ligand structure in
which the ligand are coordinate with a zinc ion in the protein, and I
want to calculated the binding free energy of this system. I have both
AMBER12 and AMBER11.

However, strangely, the MMPBSA.py in AMBER11 can work with this
structure, but which in AMBER12 can not, Would you please give me some
advice to find the reasons?

The error information of amber 12 is :
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
ValueError: unsupported format character 'V' (0x56) at index 10
Exiting. All files have been retained.

I addition, If I use AMBER11 in my calculation, how can I use the
(INP=2) option? I want the non-polar solvation free energy is modeled as
two terms: the cavity term and the dispersion term.
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Received on Thu Oct 11 2012 - 00:00:02 PDT
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