Peyman Yamin wrote:
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 guess, then, it would depend on the charges you have assigned (based on what I
read about g_sas from the help info). If you have parameterized these ether
linkages such that they are more polar, than g_sas should detect them as such.
Beyond that, I can't comment on it.
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??
I would look for publications by Connolly. I believe the algorithm derives from
that work.
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!!
Apologies :) I have GMX 3.3.3, and without checking that you had 3.3.1, I was
looking at my command line options. Maybe upgrading would serve you well?
-Justin
-------------------------------------------------------
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: [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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