Nidhi, You might be interested in this tool: http://prody.csb.pitt.edu/drugui/ Here are slide from a talk about the method: http://mmbios.org/images/workshops/HandsOn2014/Lecture3.pdf And here is a tutorial: http://prody.csb.pitt.edu/tutorials/drugui_tutorial/drugui_tutorial.pdf
I am sure that you could use GROMACS to do the simulated annealing step instead of NAMD. Tom -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
