Re: [AMBER] MMPBSA problems with Fe and Zn

From: mattia <>
Date: Mon, 01 Mar 2010 13:00:56 +0100

You should insert Zinc parameters into the file
that is in the $AMBERHOME/src/mm_pbsa/ directory.
If I don't remember bad you should only insert wdv radius and solvation
of Zinc ion.
Then you have, however, to recompile the mm_pbsa module (or maybe the
whole AMBER).

Before to do that you could try with the new I don't know
how it works with Zinc, maybe it is more "user friendly" than the old
MM_PBSA perl script.



Cristina Sisu ha scritto:
> Hi Amber users,
> I've been simulating a protein system containing Zn and Fe atoms. The Zn
> and Fe atoms are bound to residues in the protein. Therefore I've
> modified the residues in xleap to attach the respective heteroatoms. Now
> I am trying to do an MMPBSA calculation on my protein complex. I extract
> the snapshots but when I try to do an energy decomposition I get an the
> error:
> "bad atom type: Zn
> /usr/local/amber9/exe/sander -O -i -o
> sander_com.1.out -c ../snapshots/snapshot_com.crd.1 -p
> ../JMJC-noaly-2vac.prmtop not successful"
> Any ideas of how to overcome this problem?
> Thanks,
> Cristina
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Received on Mon Mar 01 2010 - 04:30:03 PST
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