Try the following way:
But you shoul get you top file and gro file without the ligand. Then If your protein has 100 residues, add you ligand as residue 101 in the gro file. After residue add the "TER" . In ddition, adding the ligand ITP file to the later part of the Gro file. -----Original Message----- From: [EMAIL PROTECTED] on behalf of ?? Sent: Tue 9/12/2006 7:07 AM To: gmx-users@gromacs.org Subject: Re:[gmx-users] merger ligand and protein to constriant What about merging the ligand the the protein by DeepView? In your mail: >From: "kanin wichapong" <[EMAIL PROTECTED]> >Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org> >To: gmx-users@gromacs.org >Subject: [gmx-users] merger ligand and protein to constriant >Date:Tue, 12 Sep 2006 13:40:59 +0200 > >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 >_______________________________________________ >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 _______________________________________________ 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
