Re: Generating binvelocities, bincoordinates, and extendedSystem files (AMBER)

From: Axel Kohlmeyer (
Date: Sun Feb 14 2010 - 04:54:11 CST

On Sun, Feb 14, 2010 at 12:01 AM, Johann Morr <> wrote:
> Hello,
> 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!
> Best,
> JM

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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