[AMBER] MMPBSA problems with Fe and Zn

From: Cristina Sisu <csds2.cam.ac.uk>
Date: Mon, 01 Mar 2010 11:53:11 +0000

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

"bad atom type: Zn
        /usr/local/amber9/exe/sander -O -i sander_com.in -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?


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Received on Mon Mar 01 2010 - 04:00:04 PST
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