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

[Peyman Yamin]

On Thursday 31 July 2008 13:34, Justin A. Lemkul wrote:
> 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!!
>
Hi Justin,
Thanks for the comments,

> 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.
>

I think I said " interacting in a hydrophilic way" and not just "interacting". 
I completely agree with you on the fact that atoms could be accessible to the 
solvent and still be hydrophobic. In the end a vacuum in the solvent is not 
that desirable, I believe. But I more or less mean "wettet" in the context of 
Physical Chemistry, particularly D. Chandler (Nature|Vol 437|29 Sep 2005).

> And, from what I understand, Triton is actually primarily hydrophobic, so a
> 50X greater hydrophobic surface area does not surprise me.
>
TritonX100 has a big head which consists of a chain of ...-CH2-O-CH2-O-... . 
This (C2H4O)n , n~10 is actually hydrophilic and is bigger than the 
hydrophobic tail of the surfactant which is a 
4-(1,1,3,3-tetramethylbutyl)-phenyl group. Based on this I expect the 
hydrophilic area should not be drastically smaller than the lipophilic part, 
as I get from g_sas. 

> > 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.

Have you - anyone else? -  by chance seen any literature refering to the 
algorithm used in g_sas??

>
> > 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.

Well, this would be nice but I don't even have such a switch in my g_sas!!

-------------------------------------------------------
Program g_sas, VERSION 3.3.1
Source code file: statutil.c, line: 799

Invalid command line argument:
-tv
-------------------------------------------------------

Peyman


>
> -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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> >
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-- 
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