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<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
face="Times New Roman" size=3>Thank you for reply.</FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
face="Times New Roman" size=3>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).<SPAN style="mso-spacerun: yes">
</SPAN>Maybe is there other way to do it.<SPAN
style="mso-spacerun: yes"> </SPAN>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. </FONT></SPAN></P>
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<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">Let say I would like to simulate membrane
protein with only two lipid molecules, how can do this.<SPAN
style="mso-spacerun: yes"> </SPAN>If anyone knows the procedure for it
please let me know.<SPAN style="mso-spacerun: yes"> </SPAN>Thank you in
advance.<SPAN style="mso-spacerun: yes">
</SPAN></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman"> <o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
face="Times New Roman" size=3>MIKE </FONT></SPAN></P><SPAN lang=EN-US
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style="mso-spacerun: yes"> </SPAN></SPAN></FONT></DIV>
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<DIV><BR><FONT face="Times New Roman" size=3>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 (</FONT><A href=""><FONT
face="Times New Roman" size=3>smithgr@cancer.org.uk</FONT></A><FONT
face="Times New Roman" size=3>)<BR>File: mdrun_make_hole.tar.gz (56919
bytes)<BR><BR><BR>which can be found on </FONT><A href=""><FONT
face="Times New Roman"
size=3>http://www.gromacs.org/contributions/index.php</FONT></A><BR><BR><FONT
face="Times New Roman"
size=3>Greetings,<BR><BR>Florian</FONT></FONT></DIV></BODY></HTML>