AMBER Archive (2004)

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

From: David A. Case (case_at_scripps.edu)
Date: Fri May 07 2004 - 10:23:33 CDT

On Wed, May 05, 2004, Sunil_Koovakkat_at_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 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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