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

From: Urszula Uciechowska <>
Date: Wed, 20 Jun 2018 12:50:11 +0200

I am using the python code.


>> 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.
> --tec3
> _______________________________________________
> AMBER mailing list

Urszula Uciechowska PhD
University of Gdansk and Medical Univesity of Gdansk
Department of Molecular and Cellular Biology
ul. Abrahama 58
80-307 Gdańsk

Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego

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