Wasn't this resolved a while ago by using BR as the term for bromine?
Jim
-----Original Message-----
From: Fábio Jorge [mailto:prifabiojorge.gmail.com]
Sent: Sunday, September 03, 2017 3:44 PM
To: amber.ambermd.org
Subject: [AMBER] Error bad atom Br
Hello.I'm trying to run the decomposition by residue but I can not.
I've tried everything! Amber 12, Amber 16, I have refined the complexes many
times, but the same error always appears: bad atom Br.Below is the error
that appears:
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
sander found! Using /home/fabio/amber12/bin/sander
mmpbsa_py_energy found! Using /home/fabio/amber12/bin/mmpbsa_py_energy
cpptraj found! Using /home/fabio/amber12/bin/cpptraj
Preparing trajectories for simulation...
4 frames were processed by cpptraj for use in calculation.
Beginning GB calculations with /home/fabio/amber12/bin/sander
calculating complex contribution...
bad atom type: br
CalcError: /home/fabio/amber12/bin/sander failed with prmtop ../complex.top!
Exiting. All files have been retained.
-------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus
causing
the job to be terminated. The first process to do so was:
Process name: [[15156,1],0]
Exit code: 1
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Received on Sun Sep 03 2017 - 17:00:02 PDT
