Re: Trying to run a setup with amber force field in NAMD

From: Aron Broom (
Date: Tue Jun 12 2012 - 21:34:09 CDT

You only need to potentially convert your coordinates. I do think that the
NAMD manual is a fantastic reference for most of these things. I suggest
going here, it not
only goes over the few things you need to run AMBER inputs in NAMD, but it
also contains the sample configuration files you were hoping for, and
explains what the relationship is between common AMBER parameters and those
in NAMD.

All you need to do to get NAMD working with AMBER inputs, is to have in
your configuration file:

amber on
parmfile [path to your *.prmtop or whatever file you would normally use -p
with when running AMBER]
ambercoor [path to your *.inpcrd or whatever file you would normally use -c
with when running AMBER]

The only catch here is that ambercoor might not accept restart files (those
coordinate files that also have velocity information), I'm not sure about
this, as whenever I run NAMD with an AMBER forcefield, I've generally
converted the coordinates to PDB first. If you do this, you can just have:

coordinates [path to your *.pdb file]

The one problem you might encounter, is that in AMBER, periodic cell
dimensions are read from the *.inpcrd file you make using LEaP. NAMD will
not do this, and you must specify those dimensions, and the cell center,

cellbasisvector1 X 0.0 0.0
cellbasisvector2 0.0 Y 0.0
cellbasisvector3 0.0 0.0 Z
cellorigin X/2 Y/2 Z/2

You can get those X, Y, Z numbers either from the very last line on your
AMBER coordinates or restart file, or by measuring the dimensions of your


On Tue, Jun 12, 2012 at 5:49 PM, scott davis <> wrote:

> Hello,
> I have looked through the tutorial and the previous messages and found the
> answers received a little hard to digest.
> I am trying to figure out how to run a simulation in NAMD using amber
> force field. I have read that different input files are needed then
> psf/pdb. I understand that yet have not been able to find a gui or utility
> to feed the psf/pdb into that will either make or allow me to make the
> files needed. Also if anyone has a sample configuration file so I have
> something to work off from. I am somewhat new to NAMD/ VMD and not very
> familiar with all of the features.
> Thank you,
> Scott Davis

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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