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
[noprogress]
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
[:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL]
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.
best
Ula
--------------------------------------------
Urszula Uciechowska PhD
University of Gdansk and Medical Univesity of Gdansk
Department of Molecular and Cellular Biology
ul. Abrahama 58
80-307 Gdańsk
Poland
-----------------------------------------
Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
http://www.ug.edu.pl/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 20 2018 - 03:00:02 PDT
