<div>Dear Alan,</div> <div> </div> <div>You are right a DPPC unit has less than 300 atoms, but I have 189 units. How can I apply PRODRG for 189 different coordinate files to convert to necessary GROMACS coordinate file? It must be very tedious.</div> <div> </div> <div>I am using ligand-enzyme tutorial for Gromacs. But for membrane-bound case I guess this tutorial is not enough to work.</div> <div> </div> <div>Best Wishes,</div> <div> </div> <div>Serdar</div> <div> </div> <div><BR><BR><B><I>Alan Dodd <anoddlad@yahoo.com></I></B> schrieb:</div> <BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid"> <STYLE type=text/css><!-- DIV {margin:0px;} --></STYLE> <DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif"> <div>Firstly, a molecule of DPPC has less than 300 atoms.</div> <div>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.</div> <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> <div> <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"
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