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