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
