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

From: Urszula Uciechowska <urszula.uciechowska.biotech.ug.edu.pl>
Date: Wed, 20 Jun 2018 11:41:08 +0200

Dear Amber users,

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 mmpbsa.py automatically strips from the trajectory certain
ions as well as magnesium ...

In _MMPBSA_normal_traj_cpptraj.out I found ...

 Reading '../top.top' as Amber Topology
        Radius Set: modified Bondi radii (mbondi)
INPUT: Reading input from 'STDIN'
  [trajin ../prod5.mdcrd 1 1000 1]
        Reading '../prod5.mdcrd' as Amber NetCDF
        Progress bar will not be used during Run.
  [strip :WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL]
    STRIP: Stripping atoms in mask

My question is how to "un-strip" the MG? Is there any script file in
mmpbsa tool that I could edit?

Thanks in advance for any help or suggestions.


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 - 03:00:02 PDT
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