Hi, On Monday 12 June 2006 17:25, Dongsheng Zhang 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!
Mixing ff types is a bad idea, i don`t know if PRODRG supports other ff like the old and depracted gmx format. I hope that there will be soon a PRODRG version which will support other force field formats, also amber ff in gromacs without heavy modifing the pdb file. As a hint: Take a look at http://www.gromacs.org/gromacs/documentation/tutorial.html for builing a system of ligand and protein. > > > 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 Greetings, Florian -- ------------------------------------------------------------------------------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Mailto: florian.haberl AT chemie.uni-erlangen.de ------------------------------------------------------------------------------- _______________________________________________ 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
