AMBER Archive (2005)

Subject: AMBER: solvent accessible surface area

From: John (john.dalmaris_at_imperial.ac.uk)
Date: Tue Apr 19 2005 - 05:45:40 CDT

Hello,

 

I am calculating the SASA of linear alkanes. I prepared all relevant files
in antechamber. Figures derived in Molsurf do not tally with the literature
for same probe radii (1.4 Å)

 

For example for the CH4 Molsurf (Amber8) gives 47.1 (only minor changes when
going from PARSE to Bondi radii)

The literature (J.Phys.Chem B, 104, 2000, 6275) gives 141.2 (using the
Connolly algorithm).

Using the VEGA software (J. Comput. Chem, Vol. 16 N3, 273-284, 1995) I get
142.7.

 

Any comment on that would be very helpful.

 

Regards,

 

John

 

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