[gmx-users] Inserting protein in Bilayer

[Justin A. Lemkul]

sunny mishra wrote:
> Hi Justin,
> 
> I have successfully created the lipid bilayer and inserted the protein
> inside that but now I feel that before doing all that I would have
> placed the water molecules or lipid molecules at some specific point.
> I want to create a lipid bilayer in which protein is inserted and on
> the top of insertion i need to put the water molecules and then at the
> bottom as well. What I don't understand is that how to place the
> molecules as per my interest because i am following martini tutorial
> and doing everything in CG and that is confusing for me now at this
> point that how to put the water molecules or lipid with protein as per
> my interest. I hope you got my question.
> 
> Thanks for all the previous help and your reply for the same would be
> highly appreciable
> 

Use genbox.  Please see my tutorial (linked before) and/or:

http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations#Adding_waters_with_genbox

There is a coarse-grain water box that would be a suitable solvent.

-Justin

> Thanks,
> 
> Sunny
> 
> On Sun, Oct 11, 2009 at 5:50 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>> sunny mishra wrote:
>>> Hi Justin,
>>>
>>> I have set up the whole system correctly but now at the final step
>>> when I do mdrun it gives me the fatal error by saying that Number of
>>> grid cells is zero. Probably the system and box collapsed.
>>>
>> Then "correctly" is debatable :)
>>
>>> Do you have any idea about this?
>>>
>> Something is unstable in your system.  See here:
>>
>> http://www.gromacs.org/Documentation/Terminology/Blowing_Up
>>
>> Beyond that, you'll have to describe what you've done as far as energy
>> minimization and equilibration, and the level of success of each of those
>> steps.
>>
>> -Justin
>>
>>> Sunny
>>>
>>>
>>>
>>> On Sun, Oct 11, 2009 at 4:45 PM, sunny mishra <mishra.sunny at gmail.com>
>>> wrote:
>>>> Hi Justin,
>>>>
>>>> Thanks for the quick reply. I am also following the martini tutorial
>>>> in order to do the CG simulations. Here are the following steps which
>>>> I am doing. Please have a look at them.
>>>>
>>>> 1) Cleaned the 1SU4.pdb file and renamed it to 1SU4_clean.pdb
>>>> 2) converted 1SU4_clean.pdb to its CG structure using awk script and
>>>> named it to 1SU4_cleancg.pdb
>>>> 3) Then created the sequence of 1SU4_clean.pdb file and also the .ssd
>>>> files.
>>>> 4) Then using the seq2itp script created the protein.itp file for 1SU4.
>>>> 5) Now I don't understand after this point what should I do because I
>>>> also have to include DSPC molecules. Where should I include them I
>>>> mean at which step?
>>>> When I make my .top file for the protein do I include DSPC molecules
>>>> there or anywhere else? Please let me know
>>>>
>>>>
>>>> Sunny
>>>>
>>>> On Sun, Oct 11, 2009 at 4:30 PM, Justin A. Lemkul <jalemkul at vt.edu>
>>>> wrote:
>>>>> sunny mishra wrote:
>>>>>> Hi All,
>>>>>>
>>>>>> I am working on the CG simulations of the proteins and lipid bilayers.
>>>>>> I am confused of how to set up the whole system for simulations. I got
>>>>>> the DSPC lipid bilayer from martini website and I have 1SU4.pdb file
>>>>>> with me. I cleaned the .pdb file and now I want to include the 14 DSPC
>>>>>> molecules in my .pdb file. I don't know if I am going in the right
>>>>>> direction or not. Please let me know how to set up the simulation for
>>>>>> the same if you have some idea. I will appreciate your help.
>>>>>>
>>>>> I wrote a tutorial for atomistic membrane protein systems:
>>>>>
>>>>>
>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html
>>>>>
>>>>> It may provide some useful information, since the premise for
>>>>> constructing
>>>>> the system is the same.  Our web server is currently down due to a power
>>>>> outage at our University, but I should have everything up and running by
>>>>> tomorrow.
>>>>>
>>>>> -Justin
>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Suny
>>>>>> _______________________________________________
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>>>>>>
>>>>> --
>>>>> ========================================
>>>>>
>>>>> Justin A. Lemkul
>>>>> Ph.D. Candidate
>>>>> ICTAS Doctoral Scholar
>>>>> 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
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> 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
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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