[AMBER] striping correctly with ante-MMPBSA.py

From: Sundar <jubilantsundar.gmail.com>
Date: Mon, 9 Oct 2017 03:24:38 -0500

Fellow AMBER users,

I am trying to generate prmtop files for complex, receptor, and ligand
using ante-MMPBSA.py
I have hard time extracting them using ante-MMPBSA.py strip_mask syntax.

My solvated.prmtop is generated from CHARMM files using CHAMBER and it has
POT and CLA for potassium and chlorine atoms. How would I get them stripped
correctly to get all the necessary files?

Is there manual for ante-MMPBSA.py on how to use the strip_mask syntax?

My protein is 1-133 (residue id) and my ligand named TYL.
POT and CLA for K+ and CL- and TIP3 for water.

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Received on Mon Oct 09 2017 - 01:30:02 PDT
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