AMBER Archive (2006)

Subject: AMBER: Na+ with GB/SA?

From: Steve Gwaltney (drg51_at_ra.msstate.edu)
Date: Thu Jan 12 2006 - 11:59:22 CST

Is is possible to do GB/SA calculations with explicit sodium ions?

I am trying to model some protein-ligand interactions. It is believed
that a sodium ion resides in the active site of the protein, and
therefore I am trying to include it in the calculations. However, if I
set "GBSA=1," the calculation crashes with the message
"bad atom type: IP." A plain GB calculation works fine. Is there a
workaround to this problem?

Thanks,
Steve 

-- 
Dr. Steven Gwaltney                  Phone: 662-325-7602
Assistant Professor                    Fax: 662-325-1618
Department of Chemistry,              Mail: Box 9573
Center for Environmental Health Sciences,   Mississippi State University
and Center for Computational Sciences       Mississippi State, MS  39762

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