Dear Amber users,
I am trying to perform binding energy decomposition energies for a
substrate bound protein system that has a Heme bound. I am using Amber14
with Ambertools15.
I understand that Sander requires the radius for Fe atom which requires
modification of the mdread2.F90 file and recompiling of sander.
I followed the instructions based on this previous query (
http://archive.ambermd.org/201412/0132.html) and modified the mdread2.F90
file and also recompiled sander. I also re-generated the complex, ligand
and receptor topologies after recompiling amber.
However, I still get the following error while performing decomp
calculations. I am able to run normal mmgb/pbsa calculations without decomp
though.
calculating complex contribution...
bad atom type: fe
File "/home/vbharadw/amber14/bin/MMPBSA.py", line 104, in <module>
app.run_mmpbsa()
File
"/home/vbharadw/amber14/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/home/vbharadw/amber14/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/home/vbharadw/amber14/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 157, in run
self.prmtop))
CalcError: /home/vbharadw/amber14/bin/sander failed with prmtop
prmtops/complex.prmtop!
Exiting. All files have been retained.
Am I missing something else too?
I will be grateful for any assistance in getting this to work.
Thank you!
--
Vivek S. Bharadwaj
Postdoctoral Researcher
National Renewable Energy Laboratory
Golden Colorado
http://inside.mines.edu/~vbharadw/
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Received on Tue Nov 24 2015 - 09:00:04 PST
