[gmx-users] g_sas, what's it all about?

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 31 13:34:17 CEST 2008



Peyman Yamin wrote:
> On Wednesday 30 July 2008 12:58, David van der Spoel wrote:
> 
>>  Peyman Yamin wrote:
> 
>>  > Hello List!
> 
>>  >
> 
>>  > I use g_sas to calculate the solvent accessible surface area of some
> 
>>  > amphiphiles. g_sas gives the result as hydrophobic area! I'm 
> wondering if
> 
>>  > the hydrophilic part is somehow not recognized, or these terms mean
> 
>>  > different things in g_sas context? For Triton, for instance, a big
> 
>>  > surface is hydrophilic, to my knowledge!
> 
>>
> 
>>  xmgrace -nxy sas.xvg
> 
> Thanks David, but what about other question marks?!
> 
> What is hydrophilic area? is it the wetted or solvated or maybe area on 
> which the solvent molecules are with less than a distance apart from 
> surface, or something else? In Triton, the length of the part which is 
> interacting in a hydrophilic way is bigger actually, but I see a result 
> of g_sas telling me that hydrophobic area is ~50 times bigger!!
> 

I believe g_sas decides hydrophobicity and hydrophilicity based on charge (and 
thus altered with the -qmax flag), from the description in the manual page.  I 
could be wrong, so someone please correct me if you are more familiar with the code.

I think you are thinking of the area somewhat backwards.  Just because part of 
the molecule is interacting with the solvent does not make it hydrophilic 
surface area.  Hence why you can have hydrophobic surface area - if, for 
example, an alkyl chain is protruding into bulk solution, it is actually 
hydrophobic, but accessible to solvent.

And, from what I understand, Triton is actually primarily hydrophobic, so a 50X 
greater hydrophobic surface area does not surprise me.

> I use ffG43a1. Is it a strange behavior to calculate SAS from a UA
> 
> trajectory?
> 

Not at all.  I have seen such analysis in the literature.

> I mean is the CHx groups' H size taken intro account ?
> 
>>  >
> 
> How is the DGsolv calculated by g_sas? and the areas ? which algorithm?
> 
> where is the code? reference?
> 

The code would be in g_sas.c, would be my guess.

>>  >
> 
> Is there any program with which one could calculate the volume enclosed
> 
> by SAS resulted from g_sas? Just if one used such and can trust any code
> 
> available anywhere??

Volumes and densities can be printed with g_sas -tv, but I don't know if this is 
what you're after.

-Justin

> 
> I see different posts in the mailing list addressing the accuracy of
> 
> g_sas! Well, I'm using gmx 3.3.1; is the accompanying g_sas reliable?
> 
>>  >
> 
> Any comment is truthfully appreciated :)
> 
>>  >
> 
> Peyman
> 
>>  >
> 
>>  >
> 
>>  P.S. Edmund Husserl believed, that we would indeed be in a nasty
> 
>>  position, if empirical science were the only kind of science possible.
> 
> -- 
> 
> Peyman Yamin
> 
> Lehrstuhl fuer Thermische Verfahrenstechnik
> 
> Universitaet Erlangen-Nuernberg
> 
> Egerlandstr. 3
> 
> 91058 Erlangen
> 
> Phone: +49(0) - 9131 - 85 27671
> 
> Mailto: peyman.yamin at cbi.uni-erlangen.de
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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