[gmx-users] lipid problem

Andreas Kukol A.Kukol at warwick.ac.uk
Thu Nov 4 11:25:30 CET 2004


First I don't think you can use prodgr to make the topology file, it does not contain the atom types LC2, LC3 used for lipid bilayer simulations. You need to get an lipid.itp file for your lipid from somewhere, e.g. Peter Tielemans website or contruct it by yourself.

1) Seperate the coordinates protein coordinates from your pdb file with a text editor and use pdb2gmx to make protein.top

2) Edit protein.top and remove #include ffgmx.itp and everything after the last definition of dihedrals apart from the position restraint entries. Save the file as protein.itp

2) Then make a new file system.top, which should look like this (in case you have Na+ ions):

; Include forcefield parameters
#include "ffgmx.itp"
#include "dmpc.itp"   <--- your lipid definition
#include "ions.itp"
#include "protein.itp"

#ifdef POSRES_P
[ position_restraints ]
; atom	type	fx	fy	fz
   8      1     0.0     0.0     1000.0
; this restraints all P8 atoms

; Include water topology
#ifdef FLEX_SPC
#include "flexspc.itp"
#include "spc.itp"

; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000

[ system ]
; Name
DMPC bilayer + water + protein + ions

[ molecules ]
; Compound        #mols
Protein                      1
DMPC		123	<--- These are the numbers of molecules of each component
SOL		3645	      you have in your system.	
Na		8

This system.top should work with grompp and the pdb file of your system.

Hope this helps

>>> kolinkolin at poczta.onet.pl 04/11/2004 09:43:41 >>>
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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