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

From: Norman Geist (
Date: Wed Jun 13 2012 - 00:50:10 CDT



you will have to use


amber on

ambercoor *for the crd coordinates


coordinates *for pdb or coor

amberparm *for the top file


You need to generate these files with the ambertools f.i. leap/xleap




Norman Geist.


Von: [] Im Auftrag
von scott davis
Gesendet: Dienstag, 12. Juni 2012 23:50
Betreff: namd-l: Trying to run a setup with amber force field in NAMD


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

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