[AMBER] Energy decomposition error

From: Renato Freitas <renatoffs.gmail.com>
Date: Fri, 19 Feb 2016 16:17:20 -0500

Dear All,

 I'm trying to run MMPBSA-Free Energy Decomposition, but for one of my
ligands, which has a fluorine atom I am getting the following error:

#################################################
Loading and checking parameter files for compatibility...
sander found! Using /opt/amber12/bin/sander
cpptraj found! Using /opt/amber12/bin/cpptraj
Preparing trajectories for simulation...
1 frames were processed by cpptraj for use in calculation.

Running calculations on normal system...

Beginning GB calculations with /opt/amber12/bin/sander
  calculating complex contribution...
 bad atom type: f
CalcError: /opt/amber12/bin/sander failed with prmtop
2Y1W-MS008_1-com_gas.prmtop!
Exiting. All files have been retained.
#################################################

Does anyone know how to fix this problem?

Thanks,

Renato
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Received on Fri Feb 19 2016 - 13:30:04 PST
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