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

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Jun 13 2012 - 00:50:10 CDT

Hi,

 

you will have to use

 

amber on

ambercoor *for the crd coordinates

or

coordinates *for pdb or coor

amberparm *for the top file

 

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

 

regards

 

Norman Geist.

 

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

 

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
 

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