AMBER Archive (2006)

Subject: AMBER: question on molsurf

From: Yongmei Pan (ypan2_at_uky.edu)
Date: Fri Oct 20 2006 - 17:38:38 CDT

Dear all:

I use two ways to calculate surface area with molsurf. One is to use command "molsurf *.pdb 1.4" (*.pdb is from ambpdb -pqr); The second way is to use mm_pbsa3.in. The parameters I use in this input file is PROBE:1.4, RADII is the file atmtypenumbers. I don't know which size mm_pbsa will use for SA calculation, the one from my SIZE file, a DELPHI parameter, or from file atmtypenumbers? Anyway, the results from two ways are different, not big. So why are they different, is this because the parameters are different? Anyone knows? Thanks!

Yongmei Pan

Pharmaceutical Sciences
College of pharmacy, University of Kentucky

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Yongmei pan
College of pharmacy, University of Kentucky

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