Dear Gromacs Users
I am simulating the interactions between ligands and DNA using GROMACS with the AMBER force field, as implemented with the AMBER PORT for GROMACS. Simulating DNA is actually very easy with this protocol, but for the ligand some problems arise. Until now we are constructing the topology manually, but this became complicated for large ligands. What is the best way to construct ligand topologies with AMBER parameters, for using with GROMACS, provided that we DO NOT have the AMBER package? Thank you very much in advance. Paulo Netz _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
