[gmx-users] Inserting protein in Bilayer

[Justin A. Lemkul]

sunny mishra 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
> 

That's what my tutorial addresses :)  Sorry it's inaccessible at the moment.  In 
short, you need to #include the relevant .itp file for the lipids, like would 
any other component of the system (solvent, ions, etc).  See Chapter 5 of the 
manual, as well as:

http://www.gromacs.org/Documentation/Include_File_Mechanism

-Justin

> 
> 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
>>> _______________________________________________
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>> --
>> ========================================
>>
>> 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
>>
>> ========================================
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www interface
>> or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
> 

-- 
========================================

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

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