Thermodynamic integration output analysis

From: Giorgio Amendola (
Date: Wed Mar 07 2018 - 05:57:08 CST

Dear NAMD users,

I'm interested in running relative binding free energy calculations for protein/ligand systems using thermodynamic integration.
However, the available perl script for the TI analysis,, doesn't work with the revised output from NAMD 2.12. So, I thought about using the 2.11 version of the software, but I'm still having problem when I run the script with the outputs from the calculation. I get errors like this one "Modification of non-creatable array value attempted, subscript -1999 at ./ line 102, <FILE> line 210477". I've tried to look into the error, and apparently it's about correctly handling the equilibration data. Other people have experienced it too, but I couldn't find a solution unfortunately.
I was wondering if any of you could give me some tips on what tools I could use to analyze the output of the 2.12 version, or maybe some version of that doesn't present this issue.


Giorgio Amendola

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