Generating binvelocities, bincoordinates, and extendedSystem files (AMBER)

From: Johann Morr (
Date: Sat Feb 13 2010 - 23:01:32 CST


I have been trying to generate the
inptut files needed to run a simulation on simple systems using the
Amber forcefield. Specifically, I am trying to create the necessary
binvelocities, bincoordinates, and extendedSystem files (sometimes named
rest.vel, rest.coor, and rest.xsc, respectively, in some tutorials). My
question is: given a PDB, how exactly can I create these 3 files for
simulation? Would I have to use tleap? If so, what specific commands
would I use, and would I need anything other than the PDB as input?
Googling this has not turned up anything very valuable so far, so hopefully someone can offer a
simple solution. Thanks!



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