AMBER: Problems with Iodine

From: <>
Date: Fri, 18 Mar 2005 15:03:38 -0600

I am having difficulties running a sander minimization with a ligand
containing iodine. It seems to pass through leap okay, but when a run is
initiated, I get the following error, followed by the usual MPI related

 bad atom type: i

If I go back and change it to a hydrogen, rerun the setup to create a new and .crd, all is fine. A diff between the leap.log files doesn't
show any differences. I am using Antechamber for the construction of a
suitable .mol2 file for leap to read in.

I am running Version 8 of AMBER compiled with "make parallel" on an SGI
Tezro. It was also tested this on an Altix 350 under version 8 and it has
the same problem.

Any thoughts on what might be causing this? Thanks in advance for your


David Maxwell, Ph.D.
Senior Research Scientist
Dept. of Experimental Diagnostic Imaging
University of Texas M.D. Anderson Cancer Center
8012 El Rio St.
Houston, TX 77054
Phone: (713)-563-9963 Fax: (713)-563-0084
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Received on Fri Mar 18 2005 - 21:53:00 PST
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