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

From: Eduard Schreiner (
Date: Tue Jun 12 2012 - 18:32:08 CDT

actually, if you have the amber ff in charmm format, you can use
psfgen to get psf/pdb and use them in the simulation. Then you do not
need to specify that it's actually amber format. Note, you will have
to adjust the 1-4 exclusions.

If you do have only the native amber ff, you can use leap, which is
part of the ambertools package to set up your system (see
corresponding manual). To my understanding the resulting crd/top files
can be directly used in namd. Check, however, the namd manual on the
format of the amber files. I do not know, if the format used now by
leap is different from the amber6/7 which namd supports


On Tue, Jun 12, 2012 at 11:49 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

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