[AMBER] MMGBSA Decomp on Heme Systems

From: Vivek Bharadwaj <vbharadw.mymail.mines.edu>
Date: Tue, 24 Nov 2015 09:46:43 -0700

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

 calculating complex contribution...

 bad atom type: fe

  File "/home/vbharadw/amber14/bin/MMPBSA.py", line 104, in <module>


line 218, in run_mmpbsa

    self.calc_list.run(rank, self.stdout)

line 82, in run

    calc.run(rank, stdout=stdout, stderr=stderr)

line 157, in run


CalcError: /home/vbharadw/amber14/bin/sander failed with 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
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Received on Tue Nov 24 2015 - 09:00:04 PST
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