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<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN
style="mso-ansi-language: PL"><FONT size=3><FONT face="Times New Roman">Hi
all!<?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office"
/><o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman">I just started learning gromacs.<SPAN
style="mso-spacerun: yes"> </SPAN>I need to simulate a GPCR in a lipid
membrane.<SPAN style="mso-spacerun: yes"> </SPAN></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
face="Times New Roman" size=3>I did all the examples at your site, but
still<SPAN style="mso-spacerun: yes"> </SPAN>have a
problem:</FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
face="Times New Roman" size=3>At first I want to try simulating rhodopsin in a
membrane.</FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
size=3><FONT face="Times New Roman"><SPAN
style="mso-spacerun: yes"> </SPAN>- I have<SPAN
style="mso-spacerun: yes"> </SPAN>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) <SPAN
style="mso-tab-count: 1">
</SPAN></FONT></FONT></SPAN></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt 36pt; TEXT-INDENT: -18pt; mso-list: l0 level1 lfo1; tab-stops: list 36.0pt"><FONT
face="Times New Roman"><SPAN lang=EN-US><FONT size=3>-</FONT><SPAN
style="FONT: 7pt 'Times New Roman'">
</SPAN></SPAN><SPAN lang=EN-US><FONT size=3>I did the topology file and
coordinate file for the protein separately.</FONT></SPAN></FONT></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt 36pt; TEXT-INDENT: -18pt; mso-list: l0 level1 lfo1; tab-stops: list 36.0pt"><FONT
face="Times New Roman"><SPAN lang=EN-US><FONT size=3>-</FONT><SPAN
style="FONT: 7pt 'Times New Roman'">
</SPAN></SPAN><SPAN lang=EN-US><FONT size=3>I did the topology file for<SPAN
style="mso-spacerun: yes"> </SPAN>one<SPAN
style="mso-spacerun: yes"> </SPAN>lipid separately and every thing seems
fine. (prodrg)</FONT></SPAN></FONT></P>
<P class=MsoNormal
style="MARGIN: 0cm 0cm 0pt 36pt; TEXT-INDENT: -18pt; mso-list: l0 level1 lfo1; tab-stops: list 36.0pt"><FONT
face="Times New Roman"><SPAN lang=EN-US><FONT size=3>-</FONT><SPAN
style="FONT: 7pt 'Times New Roman'">
</SPAN></SPAN><SPAN lang=EN-US><FONT size=3>I did coordinate file for one lipid
separately. (prodrg)</FONT></SPAN></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
face="Times New Roman" size=3>My question is:</FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
face="Times New Roman" size=3>How can I combine protein and lipids and generate
one *.gro<SPAN style="mso-spacerun: yes"> </SPAN>(coordinate file) for my
whole system. </FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
face="Times New Roman" size=3>How can I use my pdb file where I got all the
coordinates for the system.</FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US><FONT
face="Times New Roman" size=3>Should I treat every lipid as a separate molecule
or as a solvent.</FONT></SPAN></P><SPAN lang=EN-US
style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-font-family: 'Times New Roman'; mso-fareast-language: PL; mso-bidi-language: AR-SA">I
would appreciate if you could give me some suggestions what should I do
next.<SPAN style="mso-spacerun: yes"> </SPAN>Thank you in advance.
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