On Wed, May 05, 2004, Sunil_Koovakkat.berlex.com wrote:
>
> 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.
>
Here is a reply from Vickie Tsui (author of the LCPO section):
> I do remember checking with some values in the Still paper, and I remember
> doing some SA calculation for a protein at variou folding intermediates. I
> did +compare with some values in the paper, and remember reaching some sort of
> satisfactory state. Crambin (1crn) rings a bell, but 1lz1 doesn't.
> If the discrepancy of 0.7887 and 0.77887 is true according to what Sunil's
> saying, that does look like an possible type-O. I thought I was very careful
> at checking these parameters.
So, it looks like more investigation will be needed to track this down.
....regards...dac
--
==================================================================
David A. Case | e-mail: case.scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Fri May 07 2004 - 16:53:00 PDT
