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
information:
bad atom type: i
If I go back and change it to a hydrogen, rerun the setup to create a new
..top 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
help.
-Dave
_____________________________________________
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
david.maxwell.di.mdacc.tmc.edu
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Received on Fri Mar 18 2005 - 21:53:00 PST
