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

[Justin A. Lemkul]

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: 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

========================================