Re: [gmx-users] How to build a lipid bilayer in GROMACS?

2009-05-02 Thread Jack Shultz 
I don't know if this helps you, but there is a membrane plugin for VMD
which you can download for free. I've used this to insert proteins in
membranes and then use namd to run MD. I don't know what steps are
involved to make this structure compatible with GROMACS.

http://www.ks.uiuc.edu/Research/vmd/plugins/membrane/


On Sat, May 2, 2009 at 7:46 AM, Anirban Ghosh  wrote:
> Hi ALL,
>
>
>
> I have a protein pdb file. I want to put this protein molecule in a lipid
> bilayer using GROMACS. I shall be glad if anyone can kindly tell me how to
> build a lipid bilayer in GROMACS and how to embed the protein in it to get
> the final pdb of the entire system. Thanks a lot.
>
>
>
> Regards,
>
>
>
>
>
> Anirban Ghosh
>
> Grade Based Engineer
>
> Bioinformatics Team
>
> Scientific & Engineering Computing Group
>
> Centre for Development of Advanced Computing
>
> Pune, India
>
>
>
> Anirban Ghosh
> Grade Based Engineer
> Bioinformatics Team
> Centre for Development of Advanced Computing (C-DAC)
> Pune, India
>
>
> 
> Cricket on your mind? Visit the ultimate cricket website. Enter now!
> ___
> gmx-users mailing list    gmx-us...@gromacs.org
> http://www.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-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
Jack

http://www.facebook.com/home.php#/profile.php?id=832713248
http://hydrogenathome.org
___
gmx-users mailing listgmx-users@gromacs.org
http://www.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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] How to build a lipid bilayer in GROMACS?

2009-05-02 Thread Justin A. Lemkul 



Anirban Ghosh wrote:

Hi ALL,

 

I have a protein pdb file. I want to put this protein molecule in a 
lipid bilayer using GROMACS. I shall be glad if anyone can kindly tell 
me how to build a lipid bilayer in GROMACS and how to embed the protein 
in it to get the final pdb of the entire system. Thanks a lot.


 


There are several options for the lipid bilayer:

1. Obtain the coordinates from a freely-available configuration (there are many 
investigators who offer their coordinates for free)
2. Obtain the .pdb file for a single molecule, and use genconf to create a 
lattice of molecules (and even apply random rotations).  Build two leaflets, 
solvate, and equilibrate for a very long time.
3. If you have a bilayer with a similar lipid, write a script that can change 
atom names/add or delete atoms to generate the new lipid.


The caveat to all of these options is that you need proper parameters for the 
lipid of interest.  If such parameters do not exist yet, you have your work cut 
out for you.  If parameters have already been developed, then likely the 
configurations for the bilayer exist online somewhere as well.


To build the system, there are also a couple of options:

1. The InflateGRO script from Peter Tieleman's site, which I utilize in my 
membrane protein tutorial:


http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html

2. Orient your protein properly and solvate using genbox, with the bilayer 
configuration as the solvent.  This procedure can be hit-or-miss, as sometimes 
there can be atomic overlap in the output configuration, or alternately, voids 
between the protein and lipids.


-Justin



Regards,

 

 


Anirban Ghosh

Grade Based Engineer

Bioinformatics Team

Scientific & Engineering Computing Group

Centre for Development of Advanced Computing

Pune, India

 
 
*Anirban Ghosh*

*Grade Based Engineer
Bioinformatics Team
Centre for Development of Advanced Computing (C-DAC)
Pune, India
*



Cricket on your mind? Visit the ultimate cricket website. Enter now! 






___
gmx-users mailing listgmx-users@gromacs.org
http://www.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-requ...@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 listgmx-users@gromacs.org
http://www.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-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] How to build a lipid bilayer in GROMACS?

2009-05-02 Thread Anirban Ghosh 
Hi ALL,
 
I have a protein pdb file. I want to put this protein
molecule in a lipid bilayer using GROMACS. I shall be glad if anyone can kindly
tell me how to build a lipid bilayer in GROMACS and how to embed the protein in
it to get the final pdb of the entire system. Thanks a lot.
 
Regards,
 
 
Anirban Ghosh
Grade Based
Engineer 
Bioinformatics
Team 
Scientific
& Engineering Computing Group 
Centre for
Development of Advanced Computing 
Pune, India
 
 
Anirban Ghosh
Grade Based Engineer
Bioinformatics Team
Centre for Development of Advanced Computing (C-DAC)
Pune, India


  Now surf faster and smarter ! Check out the new Firefox 3 - Yahoo! 
Edition http://downloads.yahoo.com/in/firefox/?fr=om_email_firefox___
gmx-users mailing listgmx-users@gromacs.org
http://www.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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php