AMBER Archive (2009)
Subject: [AMBER] PDMED
From: Catein Catherine (askamber23_at_hotmail.com)
I am trying to do the PDMED for the dynamics simulations. After standard amber10 installation, I found pmemd and pmemd.amba directories with src subdirectory for each of them.
Do I still need to install the PDMED according to the README file too?
I would like to do the 10 ns simulation for a protein-DNA-Drug complex with explicit solvent TIP3 solvent box. Is it compatible with PDMED?
What can we do next to run the calculations? What is the step need to be done so as to use PDMED in supercomputer system?