[gmx-users] G_sas change in hydrophilic and hydrophobic surface area

[rama david]

Thank you justin


With best wishes and regards,
Rama David


On Fri, Nov 23, 2012 at 12:45 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/22/12 1:54 PM, rama david wrote:
>
>> Hi  justin,
>> Thank you for reply.
>> As per your suggestion,
>>                  The whole protein should always be the group for the
>> surface calculation. Whatever subset of those atoms (i.e. residues of
>> interest) can be the output group.
>>
>> So as per your suggestion I have to select the protein as my option 1 and
>> for output I have to select the hydrophilic residues or hydrophobic
>> residues as per my choice ....Is these is right ??? or  Am I wrong???
>>   ( That means I have to make to index file that contain two groups
>> hydrophilic and hydrophobic residues.)
>>
>> Would you please tell me why not select the protein as output, as I am
>> calculating the change  in the hydrophilic and hydrophobic surface area of
>> protein...???
>>
>>
> You can certainly do that.  Perhaps I misunderstood the original post.  I
> thought you were curious about the solvent exposure of certain residues.
>  If you only care about the evolution of total polar and nonpolar surface
> areas, then choose Protein for both groups.
>
> -Justin
>
>  As per the manual,
>>
>>       The program will ask for a group for the surface calculation and a
>> group for the output. The
>> calculation group should always consists of all the non-solvent atoms in
>> the
>> system. The output group can be the whole or part of the calculation
>> group.
>>
>>
>>
>> As two protein comes closer in simulation they formed the antiparrallel
>> beta strand, I want to find the change in hydrophilic and hydrophobic
>> surface area of protein...
>>
>>
>>
>> With Best Wishes and Regards,
>> Rama david
>>
>> On Thu, Nov 22, 2012 at 11:32 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 11/22/12 2:36 AM, rama david wrote:
>>>
>>>  Dear user ,
>>>> I simulate the two  protein in random coil position, when they come
>>>> close
>>>> they form antiparallel  beta sheet structure.
>>>>      I want to calculate the change in hydrophilic and hydrophobic
>>>> surface
>>>> area over my simulation time.
>>>> For usig g_sas  Should I have to make the different index group for
>>>> hydrophilic and hydrophobic residues
>>>> Or should only have to select the option protein both the time.
>>>>
>>>>
>>>>  The whole protein should always be the group for the surface
>>> calculation.
>>> Whatever subset of those atoms (i.e. residues of interest) can be the
>>> output group.
>>>
>>> -Justin
>>>
>>> --
>>> ==============================****==========
>>>
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Research Scientist
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.****vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>>> <h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>> >
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> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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