[AMBER] MM-GBSA for recptor-magnesium-ligand complex

From: Urszula Uciechowska <urszula.uciechowska.biotech.ug.edu.pl>
Date: Thu, 7 Jun 2018 12:24:23 +0200

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
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
startframe=1, endframe=10, interval=1,
verbose=2, keep_files=0,

the frcmod.MG file that I used for MD simulations

Mg2+ ion parameters

MG 24.3

  MG 1.5545 0.00295 MG

Many thanks

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 Thu Jun 07 2018 - 03:30:02 PDT
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