Re: AMBER: Problems with Iodine

From: Carlos Simmerling <>
Date: Fri, 18 Mar 2005 16:22:47 -0500

searching for "bad atom type" in the sander code
shows that this is an error message generated by
mdread.f, in the section that calculates parameters for the
surface area calculation. There is no parameter for
Iodine. You will need to find and add this parameter,
or else use gbsa=0 (and not do the SA calculation). wrote:

>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
>.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
>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
>The AMBER Mail Reflector
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Received on Fri Mar 18 2005 - 21:53:00 PST
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