[gmx-users] Inserting protein in Bilayer

[Mark Abraham]

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.

Some "specific point" in your workflow? Or the simulation box? Either 
way, adding waters last is usually correct because they're the easiest 
thing to add and you need only avoid placing them on top of other atoms 
or into membrane interstices.

> 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. 

The system is periodic, so there's no "top" or "bottom" - merely a 
continuous chunk of water.

> 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.

Sure, it's confusing, but you're trying to learn GROMACS and do a 
membrane simulation and do a coarse-grained simulation. Learning one of 
those at a time following simpler tutorials is very likely to help you. 
You could easily save yourself ten times the length of time you spend 
doing such "worthless" system preparation and calculations, just through 
better understanding of how things work together.

Mark

> Thanks for all the previous help and your reply for the same would be
> highly appreciable
> 
> 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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