minnale wrote:
Thanks for your prompt reply, according to you for membrane protein
protocols keep restrain only on protein but not on lipid and water, is
there any possibility to move water inside pore of the membrane when
keep restrain only on protein.
Could you please tell me
Thanks a lot in advance
Anything is possible, given the random nature of MD. It will depend
largely upon how you prepared your system. If there is a lot of void
space around your protein, then water will likely leak in over time, but
may be forced out by the hydrophobic lipid tails, if you equilibrate
long enough. If your lipids are nicely packed around your protein
(using a method like InflateGRO from Tieleman's site) then this
occurrence is less likely.
The most important thing to do is to consult the literature regarding
similar systems and take note of what those authors have done. How did
they insert the protein? How did they equilibrate the system, and for
how long?
-Justin
On Sun, 29 Jun 2008 Justin A.Lemkul wrote :
>
>
>minnale wrote:
>>
>> HI users,
>> I have embedded protein in popc bilayer and ran the
minimisation succesfully , before going equilibration I would like to
confirm one thing that how to run the equilibration with on which
system keep position restrain?
>>
>>1.we will keep position restrain on all the
systems(-DPOSRES_PROTEIN, -DPOSRES_LIPID, -DPOSRES_WATER) at a time ?
>>
>>or 2. keep position resrain on each system at a time and
>> 3.is it require to keep position restrain on water?
>>Could you tell me clearly pls
>>Thanks alot in advance
>>
>>
>
>If you "equilibrate" your system with every element of it restrained,
I think you will accomplish absolutely nothing. Typical procedures
for membrane proteins involve equilibrating with restraints on the
protein only, allowing the lipids to pack around the protein.
>-Justin
>
>>
>>HSBC
<http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/[EMAIL PROTECTED]/2204104_2196511/2199118/1?PARTNER=3&OAS_QUERY=null>
>>
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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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--
========================================
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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