<div>Thank you very much Tsjerk!!! I feel very stupid now <IMG src="http://us.i1.yimg.com/us.yimg.com/i/mesg/tsmileys2/08.gif"> <IMG src="http://us.i1.yimg.com/us.yimg.com/i/mesg/tsmileys2/01.gif">.</div> <div> </div> <div>Best regard </div> <div>Fulya<BR><BR><B><I>Tsjerk Wassenaar <tsjerkw@gmail.com></I></B> wrote:</div> <BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">Hi Fulya,<BR><BR>If your ligand is a protein, then use pdb2gmx!<BR>There's nothing special with 'being a ligand', and it's certainly not<BR>required to run it through PRODRG, because someone decided that part<BR>was to be called ligand, whereas the other part was not.<BR><BR>Tsjerk<BR><BR>On 7/3/07, fulya caglar <FULYACAGLAR@YAHOO.COM>wrote:<BR>> Hi all !<BR>> We want to MD simulation of a protein-protein complex.We can't prepare itp.<BR>> and gro files with PRODRG server.Because there are too many atoms in my<BR>> ligand
(which is a protein). How can we prepare the .itp and .gro files?Are<BR>> there any tutorial for a protein protein complex?<BR>><BR>><BR>> Best Regard<BR>> Fulya<BR>><BR>> Hacettepe University<BR>> Turkey<BR>><BR>> ________________________________<BR>> Building a website is a piece of cake.<BR>> Yahoo! Small Business gives you all the tools to get online.<BR>><BR>><BR>> _______________________________________________<BR>> gmx-users mailing list gmx-users@gromacs.org<BR>> http://www.gromacs.org/mailman/listinfo/gmx-users<BR>> Please search the archive at http://www.gromacs.org/search before posting!<BR>> Please don't post (un)subscribe requests to the list. Use the<BR>> www interface or send it to gmx-users-request@gromacs.org.<BR>> Can't post? Read<BR>> http://www.gromacs.org/mailing_lists/users.php<BR>><BR><BR><BR>-- <BR>Tsjerk A. Wassenaar, Ph.D.<BR>Junior UD (post-doc)<BR>Biomolecular NMR, Bijvoet
Center<BR>Utrecht University<BR>Padualaan 8<BR>3584 CH Utrecht<BR>The Netherlands<BR>P: +31-30-2539931<BR>F: +31-30-2537623<BR>_______________________________________________<BR>gmx-users mailing list gmx-users@gromacs.org<BR>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>Please search the archive at http://www.gromacs.org/search before posting!<BR>Please don't post (un)subscribe requests to the list. Use the <BR>www interface or send it to gmx-users-request@gromacs.org.<BR>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR></BLOCKQUOTE><BR><p> 
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