[gmx-users] lipid problem

Kolin kolinkolin at poczta.onet.pl
Thu Nov 4 10:43:41 CET 2004

Thank you for reply.

But in my case I don't need to make a hole in the lipid bilayer, I have all the coordinates in he pdb file. (in this pdb file protein and lipids are in proper place).  Maybe is there other way to do it.   I wonder how can I mix coordinate files for lipids from prodrg with coordinate file for protein generated using pdb2gmx to make one coordinate file for the whole system. 


Let say I would like to simulate membrane protein with only two lipid molecules, how can do this.  If anyone knows the procedure for it please let me know.  Thank you in advance.   





> Hi all!
> I just started learning gromacs.  I need to simulate a GPCR in a lipid
> membrane.
> I did all the examples at your site, but still  have a problem:
> At first I want to try simulating rhodopsin in a membrane.
>       - I have  one pdb file with rhodopsin and some lipids and water
> after a MD simulation in NAMD (so all the coordinates are there) (I
> want to try it as a example)
> -         I did the topology file and coordinate file for the protein
> separately.
> -         I did the topology file for  one  lipid separately and every
> thing seems fine. (prodrg)
> -         I did coordinate file for one lipid separately. (prodrg)
> My question is:
> How can I combine protein and lipids and generate one *.gro  (coordinate
> file) for my whole system.
> How can I use my pdb file where I got all the coordinates for the system.
> Should I treat every lipid as a separate molecule or as a solvent.
> I would appreciate if you could give me some suggestions what should  I do
> next.  Thank you in advance.

i think you are searching for this

 mdrun modified to make a hole in a lipid bilayer
A modified version of mdrun that can be used to make a hole in a lipid
bilayer that is the right shape to drop in the membrane protein of your
choice. It does this by reading a molecular surface file made by Grasp or
MSMS. It can also make a cylindrical hole. Tar file contains
Uploaded 15:19 October 15, 2002 by Graham R. Smith (smithgr at cancer.org.uk)
File: mdrun_make_hole.tar.gz (56919 bytes)

which can be found on http://www.gromacs.org/contributions/index.php


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