[gmx-users] Inserting protein in Bilayer

[sunny mishra]

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
>> _______________________________________________
>> 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
>