Hi, you can also have different chains (Protein and Ligand) and constrain them. Using the -merge option you can merge the ligand into the protein but for that you need the topology for the ligand (as rtf, not from prodrg). If you use Prodrg-topology you first set up the protein without ligand. Then you include the topology for the ligand into the protein topology (#include XXX.top) and also the coordinates in the protein-gro-file. Then you can proceed with adding water, ions, etc. Then you can also apply position-restraints.
By the way, as far as I know Sonja Schlimme has used a similar kind of setup in her MD simulations. So you could also ask her. Best regards, Björn > Hi all > I already look in the turorial however that is not the thing that I try > to look for. I would like to merge the ligand into the protein and then > make the contrain between two atoms, one from the liagand and one from the > protein. However, as far as I know, I can do the constraint or restraint > just in the one chain. I cant do that with the different chain. So that i > try to merge ligand chain and protein chain. I tried to do that with > pdb2gmx but it is not work. So that i would like to know is there any way > to merge the ligand chain with the protein chain. > Thanks for all your suggstions > > Best Regard > Kanin -- Björn Windshügel Department of Pharmaceutical Chemistry University of Kuopio Harjulantie 1 70211 Kuopio, FINLAND Phone: (+358) 17 162463 Fax: (+358) 17 162456 _______________________________________________ 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