From: Beale, John <John.Beale.stlcop.edu>
Date: Thu, 1 Apr 2010 05:39:26 -0500

Using Amber 10, I am trying to set up a calculation of solvent
accessible surface area for a small protein. I understand that I need to
set imin=5, igb > 0, gbsa=2, and surften=1, and the SASA will be given
by the Esurf value. I am still unclear as to what I need to do. Would
someone be so kind as to send me an example sander input file for
calculation of SASA using the above parameters?


A problem that I have noted when I try to do this, is that when I enter
the input coordinate sets (inptraj) using the -y parameter in sander, I
get an error message that says "-y" is an invalid flag. Has this been
changed to something else?




John M. Beale, Jr., Ph,D.

Professor of Medicinal Chemistry and Pharmacognosy

St. Louis College of Pharmacy

4588 Parkview Place

St. Louis, Missouri 63110


Cell: (314)-315-0409

FAX (314) 446-8460






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Received on Thu Apr 01 2010 - 04:00:03 PDT
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