<table cellspacing='0' cellpadding='0' border='0' ><tr><td valign='top' style='font: inherit;'><P>you may try prodrg beta to get Gromos96 ff for your lipid.</P>
<P> </P>
<P>serdar<BR></P>
<P><BR>--- Rebeca García Fandiño <I><regafan@hotmail.com></I></B> schrieb am <B>Fr, 11.7.2008:<BR></P>
<BLOCKQUOTE style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: rgb(16,16,255) 2px solid">Von: Rebeca García Fandiño <regafan@hotmail.com><BR>Betreff: [gmx-users] topology for a membrane + protein<BR>An: gmx-users@gromacs.org<BR>Datum: Freitag, 11. Juli 2008, 11:14<BR><BR>
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<P class=EC_EC_MsoNormal><SPAN lang=EN-GB><FONT size=3><FONT color=#000000><FONT face="Times New Roman">Hello,</FONT></FONT></FONT></SPAN></P>
<P class=EC_EC_MsoNormal><SPAN lang=EN-GB><FONT size=3><FONT color=#000000><FONT face="Times New Roman">I am a new user of Gromacs, and I am trying to simulate a system of a membrane composed by POPC, cholesterol and sphingomyelin and a protein. I am using lipid.itp, but it includes ffgmx.itp, and I have read it is deprecated, so I am having a lot of problems to introduce the protein topology with ffG43a1 or opls, without using ffgmx.itp also for the protein. </FONT></FONT></FONT></SPAN></P>
<P class=EC_EC_MsoNormal><SPAN lang=EN-GB><FONT size=3><FONT color=#000000><FONT face="Times New Roman">I would like to know which is the recommendation, because I am a bit confused about this, an in the case of using a different force field from the deprecated ffgmx for the protein, does anybody know where I could get the paremeters for the Berger lipids constructed with a more modern forcefield than ffgmx?</FONT></FONT></FONT></SPAN></P>
<P class=EC_EC_MsoNormal><SPAN lang=EN-GB><FONT size=3><FONT color=#000000><FONT face="Times New Roman">I hope somebody could help me, I will really appreciate your advices.</FONT></FONT></FONT></SPAN></P>
<P class=EC_EC_MsoNormal><SPAN lang=EN-GB><FONT size=3><FONT color=#000000><FONT face="Times New Roman">Best wishes, </FONT></FONT></FONT></SPAN></P>
<P class=EC_EC_MsoNormal><SPAN lang=EN-GB><FONT face="Times New Roman" color=#000000 size=3> </FONT></SPAN></P>
<P class=EC_EC_MsoNormal><FONT face="Times New Roman" color=#000000 size=3>Rebeca Garcia</FONT></P>
<P class=EC_EC_MsoNormal><FONT face="Times New Roman" color=#000000 size=3>Parc Cientific de Barcelona </FONT></P>
<P class=EC_EC_MsoNormal><FONT face="Times New Roman" color=#000000 size=3>Universidad de Barcelona</FONT></P>
<P class=EC_EC_MsoNormal><FONT face="Times New Roman" color=#000000 size=3>regafan@hotmail.com</FONT></P><BR>
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