[gmx-users] Inserting protein in Bilayer

[Justin A. Lemkul]

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

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