Dear Yang, Really thanks for the help. Distance constraint can describe the bond length between ligand and protein, how about other propery of covalent bond? Maybe I missed something of your message.
Yours Tanping --- Yang Ye <[EMAIL PROTECTED]> wrote: > you might want to try distance constraint. > > On 11/7/2007 5:11 AM, Tanping Li wrote: > > Dear all, > > > > I searched the mailling list, and still can't find > a > > way to set up my system: a ligand covalently bond > to > > protein. > > > > I don't know if there is a easier way to do this. > What > > I can think of is: > > > > > > 1) Add a bond I like in the specbond.dat file; > > 2) Add a block for ligand in the rtp file; > > 3) run pdb2gmx, gromacs will treat protein and > ligand > > a one chain since it can see the bond in the > > specbond.dat. > > > > > > I just wonder if there is a eaiser way to add a > ligand > > to rtp file? When I run Dundee PRODRG2, I get a > .itp > > file. Is there some way to change this into rtp > > format? It is not trival to write a rtp manually. > > Really appretiate your help. > > > > Yours > > Tanping > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > http://www.gromacs.org/search before posting! > > 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 [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/search before posting! > 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 [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
