Re: [AMBER] How to "un-strip" the MG* atom from mmpbsa

From: Thomas Cheatham <>
Date: Wed, 20 Jun 2018 04:42:53 -0600 (MDT)

> I have an MG ion in my gag-receptor complex. However after running mmpbsa
> as I wrote before I was obtaining an mismatch error. The reason for that
> was that the automatically strips from the trajectory certain
> ions as well as magnesium ...
> [strip :WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL]

This appears to be the older MM-PBSA perl code that hard codes in ions to
strip (noting that some of the ion names are legacy). One could modify
the perl code, however better would be to learn the newer and more
flexible Python code (chapter 31 of recent AMBER manual).

With this code, I would separately create my own stripped trajectories
and prmtops for complex, receptor, and ligand. Alternatively, you could
specify the strip_mask yourself.


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Received on Wed Jun 20 2018 - 04:00:02 PDT
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