On Thu, Mar 28, 2013 at 8:18 AM, Saravanan <[email protected]> wrote:
> Thank you.. I hoped it would be simpler. how do I go about creating unified > protein-ligand [moleculartype] directives. Can you suggest any material > available on this topic? that would be extremely helpful. > > Depending on the complexity of the ligand, you may be able to do it by hand by simply adding the ligand parameters after the protein in all relevant directives of the Protein [moleculetype]. Otherwise, you will need to create an .rtp entry for the ligand and use pdb2gmx command line options to create the merged topologies (using, e.g. chain identifiers to indicate that they should be placed in the same [moleculetype] directive). In this case, refer to http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field . This is a rather advanced topic, so do as much tutorial material and other simulations as you can to familiarize yourself with a "standard" Gromacs workflow. You should also read Chapter 5 of the manual thoroughly to understand topology organization. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
