AMBER Archive (2005)

Subject: Re: AMBER: solvent accessible surface area

From: Ray Luo (rluo_at_uci.edu)
Date: Mon Apr 18 2005 - 21:12:54 CDT

John,

You can use pbsa to calculate SASA, please use npbverb=1 to print it out.

Best,
Ray

John wrote:

> 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
>
>
> 

-- 
====================================================
Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
Fax: (949)824-8551          e-mail: rluo_at_uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
====================================================

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