Dear amber users,
I was wondering how could I calculate the MM-GBSA for a complex where in
receptor I have Mg2+ ion and ligand. I run MD for 20ns using AMBER 16
however after running MM-GBSA I am still getting an error message:
CalcError: /users/work/czarek/amber16/bin/sander failed with prmtop
complex.top!
Error occured on rank 0.
Exiting. All files have been retained.
I have tried different igb models and raddii bondi but still did not work.
I do not have any more clue what to check or test more. Do I need to add
something in the mmgbsa parameters file? If yes where?
Could anyone one let me know what should I check more or do?
My MM-GBSA input:
Input file for GB/decomposition calculation
&general
startframe=1, endframe=10, interval=1,
verbose=2, keep_files=0,
/
&gb
igb=2,
/
&decomp
idecomp=2
/
the frcmod.MG file that I used for MD simulations
Mg2+ ion parameters
MASS
MG 24.3
NONBON
MG 1.5545 0.00295 MG
Many thanks
Urszula
--------------------------------------------
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/
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Received on Thu Jun 07 2018 - 03:30:02 PDT
