[gmx-developers] SAS or SES algorithm in GROMACS

[H.J.Risselada]

On Tue, 23 Jan 2007 19:02:33 +0100
  David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> Martin Höfling wrote:
>> Am Dienstag, 23. Januar 2007 16:53 schrieb Tsjerk 
>>Wassenaar:
>> 
>> Thanks Tsjerk for your quick answer.
>> 
>>> g_sas can generate the connely surface. You can run 
>>>through the code
>>> for the routines you need.
>> 
>> I checked through the code and the output. I tried 
>>several settings but the 
>> surface is triangulated too irregular. Also there are 
>>some holes it where no 
>> dots are.
>> 
>> But your suggestion was worth a try.
>> 
>> Cheers
>> 	Martin
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> have you checked the flags? how about -ndots 96?
> 
> -- 
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular 
>Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org 
>  http://folding.bmc.uu.se
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I once used the algorithm implemented in g_sas for 
calculating the local surface normals for determining the 
S parameter (the magnitude of matching) between 2 
interacting surfaces for a collegue of mine. (version 3.3)
The algoritm in g_sas is far to cruel to do this job. It 
gives a very rough estimate of the surface. In fact, in 
some cases the surface dots completely missed a whole side 
chain while in oder cases it matched very porely no matter 
which flags you set.  Therefore the S values gave us 
rubish.
This might have been a bug or simply a limitation in the 
approximation of the surface. The "ball roll" or the
"sphere overlab" algorithm have diffirent limitations.
For some proteins (the more glocular onces), however, 
g_sas will probaly do a better job then for others.

Ofcourse it will also have an affect on the values of the 
solvent accesible surface, although the scaling might 
still be correct if this error is more or less constant.
Infact as my collegue checked this, g_sas, nacces or VMD 
gave him quite different values for the solvent accesible 
surface but globaly similar scaling.

greetings,

Jelger