From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Feb 14 2010 - 04:54:11 CST
On Sun, Feb 14, 2010 at 12:01 AM, Johann Morr <rand132456_at_yahoo.com> wrote:
> 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
you dont have to create those files initially. they will be created by namd.
you need them to seamlessly restart a run. have a closer look at the tutorials.
> 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!
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://sites.google.com/site/akohlmey/ Institute for Computational Molecular Science Temple University, Philadelphia PA, USA.
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