AMBER Archive (2005)

Subject: RE: AMBER: solvent accessible surface area

From: John (john.dalmaris_at_imperial.ac.uk)
Date: Tue Apr 19 2005 - 07:22:04 CDT


I guess Molsurf calculates solvent excluding surface and not accessible
surface.

 

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
John
Sent: 19 April 2005 11:46
To: amber_at_scripps.edu
Subject: AMBER: solvent accessible surface area

 

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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