<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><P>Firstly, a molecule of DPPC has less than 300 atoms.</P>
<P>Secondly, I'd suggest you look for stuff by Tieleman, White, or Sansom. Googling/literature searching any of these names with "membrane" should give you some rough pointers on how it's been done in the past.</P>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">There is no official membrane tutorial, however. There is a ligand/receptor one out there somewhere I think?<BR><BR>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">----- Original Message ----<BR>From: serdar durdagi <durdagis@yahoo.de><BR>To: Discussion list for GROMACS users <gmx-users@gromacs.org><BR>Sent: Thursday, March 20, 2008 2:00:49 AM<BR>Subject: [gmx-users] tutorial for membrane-bound systems<BR><BR>
<DIV>Dear all,</DIV>
<DIV> </DIV>
<DIV>I would like to make MD simulations of a drug at the binding site of the receptor sorrounded by DPPC.</DIV>
<DIV>pdb coordinate file of all DPPC units (189 units, 1 unit has 130 atoms) are described seperately. I was using Dundee PRODRG server for generating .itp and drgpoh2.pdb files for the drug. Since this program is limited to convert files up to 300 atoms, I couldn't use it for the DPPC units for constructing a full drgpoh2.pdb file for the DPPC.</DIV>
<DIV> </DIV>
<DIV>Is there any tutorial of GROMACS for this kinds of systems?</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV>Kind Regards,</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV>Serdar Durdagi</DIV>
<DIV> </DIV>
<DIV> </DIV>
<P>
<HR SIZE=1>
<A href="http://uk.rd.yahoo.com/evt=51524/*http://de.mobile.yahoo.com/interstitial?refer=e00127" target=_blank rel=nofollow><B>Lesen Sie Ihre E-Mails jetzt einfach von unterwegs.</B></A>.<!-- kill -->
<DIV><BR><BR>-----Inline Attachment Follows-----<BR><BR>_______________________________________________<BR>gmx-users mailing list <A href="mailto:gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR><A href="http://www.gromacs.org/mailman/listinfo/gmx-users" target=_blank>http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>Please search the archive at <A href="http://www.gromacs.org/search" target=_blank>http://www.gromacs.org/search</A> before posting!<BR>Please don't post (un)subscribe requests to the list. Use the <BR>www interface or send it to <A href="mailto:gmx-users-request@gromacs.org" ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.<BR>Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php" target=_blank>http://www.gromacs.org/mailing_lists/users.php</A></DIV></DIV><BR></DIV></div><br>
<hr size=1>Never miss a thing. <a href="http://us.rd.yahoo.com/evt=51438/*http://www.yahoo.com/r/hs"> Make Yahoo your homepage.</a></body></html>