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<DIV>Thank you for reply. I will try it. :)</DIV>
<DIV>mike</DIV>
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<DIV>Message: 9<BR>Date: Thu, 04 Nov 2004 11:44:32 +0100<BR>From: "Steffen
Haerterich"<BR><<A
href="mailto:haerterich@apollo1.pharmazie.uni-erlangen.de">haerterich@apollo1.pharmazie.uni-erlangen.de</A>><BR>Subject:
Re: [gmx-users] lipid problem<BR>To: <A
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>Message-ID:
<<A
href="mailto:418A161F.4708.9EC8E1@apollo1.pharmazie.uni-erlangen.de">418A161F.4708.9EC8E1@apollo1.pharmazie.uni-erlangen.de</A>><BR>Content-Type:
text/plain; charset=ISO-8859-1<BR><BR>Hallo!<BR>I usually do the following. It's
quite simple. Just pack all your <BR>coordinates (Protein + Lipids + Solvent)
together into one huge .gro file <BR>(Copy'n'Paste with a text editor or
anything else). For example Protein-<BR>Lipids-Water. Try not to mix them
because then you'll end up with a <BR>very complicated setup.<BR>Next thing to
do is to adapt your topology.<BR>It is quite nice if you have "external"
topologies of your molecules.<BR>(Normally signed as .itp files, nothing more
than a topology-file <BR>truncated to the core of the molecule
description)<BR>In your case these will probably be one for rhodopsin, one for a
lipid-<BR>molecule and one for water (which is normally already included in the
<BR>topology created by pdb2gmx).<BR>You then "#include " the missing topologies
in your main topologie-file <BR>in the correct order used within your .gro file
(I don't know if the correct <BR>order is really necessary)<BR>Finally at the
end of the topology adapt the [molecules] section to fit <BR>your system
e.g.:<BR><BR>[molecules]<BR>Protein
1<BR>DPPC
128<BR>SOL 3245<BR><BR>This
tells grompp the order and amount of the different molecules in <BR>the huge
.gro file.<BR>BTW.: It might be usefull to renumber your .gro file after all
that copy-<BR>and-pasting (simply use the -renumber option with
genconf)<BR><BR>I hope this chaotic description is of some help to
you.<BR><BR>Steffen<BR><BR><BR><BR>On 4 Nov 2004 at 10:43, Kolin
wrote:<BR><BR>> <BR>> Thank you for reply.<BR>> But in my case I donTt
need to make a hole in the lipid bilayer, I have all the coordinates in he
<BR>> pdb file. (in this pdb file protein and lipids are in proper place).
Maybe is there other way to do <BR>> it. I wonder how can I mix coordinate
files for lipids from prodrg with coordinate file for <BR>> protein generated
using pdb2gmx to make one coordinate file for the whole system. <BR>>
<BR>> Let say I would like to simulate membrane protein with only two lipid
molecules, how can do <BR>> this. If anyone knows the procedure for it please
let me know. Thank you in advance. <BR>> <BR>> MIKE <BR>> <BR>>
<BR>> <BR>> <BR>> <BR>> hi<BR>> <BR>> > Hi all!<BR>>
><BR>> > I just started learning gromacs. I need to simulate a GPCR in
a lipid<BR>> > membrane.<BR>> ><BR>> > I did all the examples
at your site, but still have a problem:<BR>> ><BR>> > At first I
want to try simulating rhodopsin in a membrane.<BR>> ><BR>> > - I
have one pdb file with rhodopsin and some lipids and water<BR>> > after a
MD simulation in NAMD (so all the coordinates are there) (I<BR>> > want to
try it as a example)<BR>> ><BR>> > - I did the topology file and
coordinate file for the protein<BR>> > separately.<BR>> ><BR>>
> - I did the topology file for one lipid separately and every<BR>> >
thing seems fine. (prodrg)<BR>> ><BR>> > - I did coordinate file for
one lipid separately. (prodrg)<BR>> ><BR>> > My question is:<BR>>
><BR>> > How can I combine protein and lipids and generate one *.gro
(coordinate<BR>> > file) for my whole system.<BR>> ><BR>> >
How can I use my pdb file where I got all the coordinates for the
system.<BR>> ><BR>> > Should I treat every lipid as a separate
molecule or as a solvent.<BR>> ><BR>> > I would appreciate if you
could give me some suggestions what should I do<BR>> > next. Thank you in
advance.<BR>> <BR>> i think you are searching for this<BR>> <BR>>
mdrun modified to make a hole in a lipid bilayer<BR>> A modified version of
mdrun that can be used to make a hole in a lipid<BR>> bilayer that is the
right shape to drop in the membrane protein of your<BR>> choice. It does this
by reading a molecular surface file made by Grasp or<BR>> MSMS. It can also
make a cylindrical hole. Tar file contains<BR>> documentation.<BR>>
Uploaded 15:19 October 15, 2002 by Graham R. Smith (<A
href="mailto:smithgr@cancer.org.uk">smithgr@cancer.org.uk</A>)<BR>> File:
mdrun_make_hole.tar.gz (56919 bytes)<BR>> <BR>> <BR>> which can be
found on <A
href="http://www.gromacs.org/contributions/index.php">http://www.gromacs.org/contributions/index.php</A><BR>>
<BR>> Greetings,<BR>> <BR>>
Florian<BR><BR><BR><BR><BR>------------------------------<BR><BR></DIV></BODY></HTML>