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: [EMAIL PROTECTED]
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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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