So if I generate an .itp with PRODRG, and link it in the .top file, then grompp can use the original .pdb file? Or it's not that simple?<br><br><div><span class="gmail_quote">On 6/12/06, <b class="gmail_sendername">Alan Dodd
</b> <<a href="mailto:anoddlad@yahoo.com">anoddlad@yahoo.com</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">It's entirely possible to mix and match forcefield
<br>files to create a hybrid forcefield - the lipid<br>forcefield I use has OPLS parameters for the<br>headgroups, custom parameters for lipid tails, and GMX<br>parameters for everything else. As long as the hybrid<br>forcefield is internally consistent, it will work.
<br>How accurate it is, is another matter...<br>So yes, you can technically use PRODRG itps with other<br>forcefields, but bear in mind firstly, atomtypes etc<br>in your itp file will all need checking to make sure<br>they are accounted for in both forcefields (are
<br>'default' values the same in one forcefield as<br>another, for instance? Probably not - you may need to<br>alter the itp to describe defaults explicitly), and<br>secondly that they are not designed to be used in the<br>
same system.<br><br>--- Dongsheng Zhang <<a href="mailto:dong@pampas.chem.purdue.edu">dong@pampas.chem.purdue.edu</a>><br>wrote:<br><br>> Sear Mark,<br>><br>> Since PRODRG server only generates a itp file by
<br>> using gromos type force<br>> field, do I have to use gromos force field for my<br>> whole protein-ligand<br>> system if my ligand force field parameters are got<br>> from PRODRG? In<br>> another word, can I mix two different force field
<br>> (one for protein, one<br>> for ligand) in one system? Thanks!<br>><br>><br>> Best Wishes!<br>><br>> Dongsheng<br>><br>><br>><br>> On Tue, 2006-06-13 at 01:16 +1000, Mark Abraham<br>> wrote:
<br>> > Tamas Horvath wrote:<br>> > > As I understand, if there are "special"<br>> molecules in a pdb file, pdb2gmx<br>> > > cannot convert it. However, PRODRG can create an<br>> *.itp file for that
<br>> > > molecule, so that I can include it in the<br>> generated topology file. But<br>> > > how can I place the molecule in it's original<br>> position? Or even better,<br>> > > how can I convert the original ("full") .pdb
<br>> file for gromacs?<br>> ><br>> > Where's the problem? pdb2gmx makes a .top file for<br>> your non-special<br>> > system, you #include the .itp file for your<br>> special part. There's<br>> > nothing about atomic positions yet.... have a look
<br>> at a .top file. Now<br>> > grompp takes the .top and some file with atomic<br>> positions and makes a<br>> > .tpr file. Same general procedure as normal.<br>> ><br>> > Mark<br>> > _______________________________________________
<br>> > gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> > <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users
</a><br>> > Please don't post (un)subscribe requests to the<br>> list. Use the<br>> > www interface or send it to<br>> <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> > Can't post? Read<br>> <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br>> _______________________________________________<br>> gmx-users mailing list
<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please don't post (un)subscribe requests to the
<br>> list. Use the<br>> www interface or send it to<br>> <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read<br>> <a href="http://www.gromacs.org/mailing_lists/users.php">
http://www.gromacs.org/mailing_lists/users.php</a><br>><br><br><br>__________________________________________________<br>Do You Yahoo!?<br>Tired of spam? Yahoo! Mail has the best spam protection around<br><a href="http://mail.yahoo.com">
http://mail.yahoo.com</a><br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
http://www.gromacs.org/mailman/listinfo/gmx-users</a><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">gmx-users-request@gromacs.org
</a>.<br>Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br>