[gmx-users] (no subject)
kolinkolin at poczta.onet.pl
Thu Nov 4 20:03:24 CET 2004
Thank you for reply. I will try it. :)
Date: Thu, 04 Nov 2004 11:44:32 +0100
From: "Steffen Haerterich"
<haerterich at apollo1.pharmazie.uni-erlangen.de>
Subject: Re: [gmx-users] lipid problem
To: gmx-users at gromacs.org
Message-ID: <418A161F.4708.9EC8E1 at apollo1.pharmazie.uni-erlangen.de>
Content-Type: text/plain; charset=ISO-8859-1
I usually do the following. It's quite simple. Just pack all your
coordinates (Protein + Lipids + Solvent) together into one huge .gro file
(Copy'n'Paste with a text editor or anything else). For example Protein-
Lipids-Water. Try not to mix them because then you'll end up with a
very complicated setup.
Next thing to do is to adapt your topology.
It is quite nice if you have "external" topologies of your molecules.
(Normally signed as .itp files, nothing more than a topology-file
truncated to the core of the molecule description)
In your case these will probably be one for rhodopsin, one for a lipid-
molecule and one for water (which is normally already included in the
topology created by pdb2gmx).
You then "#include " the missing topologies in your main topologie-file
in the correct order used within your .gro file (I don't know if the correct
order is really necessary)
Finally at the end of the topology adapt the [molecules] section to fit
your system e.g.:
This tells grompp the order and amount of the different molecules in
the huge .gro file.
BTW.: It might be usefull to renumber your .gro file after all that copy-
and-pasting (simply use the -renumber option with genconf)
I hope this chaotic description is of some help to you.
On 4 Nov 2004 at 10:43, Kolin wrote:
> Thank you for reply.
> But in my case I donTt 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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