AMBER Archive (2004)

Subject: AMBER: Solvent accessible surface area(LCPO) computation

From: Sunil_Koovakkat_at_berlex.com
Date: Wed May 05 2004 - 16:51:59 CDT

The results of solvent accessible surface area computation using AMBER 6
appears to have some differences with the work of Still and coworkers. The
results from the two cases that i have tried are as follows.

                        Amber 6 J. Weiser, P.S. Shenkin and W. C.
Still,J.Comp.chem 20, 217(1999)

      Crambin(1crn) 3008.34 3064.9

      Human lysozyme(1lz1) 6235.52 6681.9

Any ideas about what i should look at more carefully with respect to the
input ? In mdread.f , the P1 parameter for C sp3 with 1 bonded neighbor is
0.7887 while the corresponding number in the LCPO
paper(J.Comp.chem.20,217,1999) is 0.77887. This difference in the P1
parameter does not appear to be the source of the difference in the
computed surface area.

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