Hi,
I want to do MM/GBSA of a structure with Mn2+. So I followed the
instructions of an older post and modified
amber16/AmberTools/src/sander/mdread2.F90
file as described for Fe at:
http://archive.ambermd.org/201303/0229.html
using the radius of Mn2+ with coordination V as in the structure:
http://abulafia.mt.ic.ac.uk/shannon/radius.php?Element=Mn
After that I recompiled AmberTools16. However, MMPBSA.py still fails with
the following error:
bad atom type: Mn
> File "/home/thomas/Programs/amber16/bin/MMPBSA.py", line 100, in <module>
> app.run_mmpbsa()
> File
> "/home/thomas/Programs/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py",
> line 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File
> "/home/thomas/Programs/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> line 82, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File
> "/home/thomas/Programs/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
> line 157, in run
> self.prmtop))
> CalcError: /home/thomas/Programs/amber16/bin/sander failed with prmtop
> complex.prmtop!
> Exiting. All files have been retained.
Is there any other file I must modify?
Btw, every time I want to calculate MM/GBSA energies of structures with
metal ions that have varying coordination number, I need to edit the radii
in the source code and recompile?
thanks,
Thomas
--
======================================================================
Thomas Evangelidis
Research Specialist
CEITEC - Central European Institute of Technology
Masaryk University
Kamenice 5/A35/1S081,
62500 Brno, Czech Republic
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Mon Sep 12 2016 - 18:30:03 PDT
