minnale wrote:
Thanks for reply Justin, can I do this way first I will keep PR on popc
later protein, I dont want keep PR on water.Can I do like this?
You could, but I don't see the point. In equilibrating membrane protein
systems, it is very important to optimize the lipid positions around the protein
at the outset of the simulation (i.e., packing). So allowing the protein to
move unrestrained while restraining the lipids makes no sense (and you will
probably generate some artificial interactions). You will want to apply PR to
the protein, allowing the lipids to pack around it, then remove the PR from the
protein and proceed with data collection.
-Justin
Thanks in advance.
On Tue, 16 Sep 2008 Justin A.Lemkul wrote :
>
>
>minnale wrote:
>>Thanks Justin for your kind reply, you misunderstood my query,now I
am asking you clearly that, while doing membrane protein equilibration
steps on which system( either protein or membrane or both) I have keep
to position restrain? is there any conventional way to keep restrain? or
it can change according to ourselves. I hope you understood my problem.
>>Can you give me suggestion
>
>You can restrain whatever you like; typically just the protein is
restrained. Check the literature for common protocols.
>
>-Justin
>
>>Thanks in advance.
>>
>>
>>
>>
>> >minnale wrote:
>> >> Hi all,
>> >>I embedded protein into popc bilayer by using genbox command, in
equilibration I want keep restrain only on protein but not on popc? can
I do like this or is there any manditory steps to run membrane protein
equibration, if it is there, Can you tell me please.
>> >>Thank you.
>> >
>> >Use "define = -DPOSRES" which is specified in the .top from
parameterizing the protein under pdb2gmx. There's nothing special
(necessarily) for doing a membrane protein system, since all the
topology information for the protein generally comes before the
lipid/solvent stuff, anyway.
>> >
>> >-Justin
>> >
>> >>
>> >>
>> >>
>> >>Ebay
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>> >>
>> >>
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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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--
========================================
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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