From: Peter Freddolino (
Date: Wed Dec 20 2006 - 13:59:28 CST

Hi Marcelo,
have you run across any tools besides namdenergy that this is a problem for?

In the case of namdenergy, I had not realized people would be wanting to
use it with AMBER parameters. I have never used AMBER parameters, so I
would appreciate it if you could send me a sample set of input files
(parameters, coordinates, namd input, and whatever else you need for the
run) to me so I can use the proper syntax and test it with NAMDEnergy. I
should then be able to send you a hacked version that will work for your
purposes, and add proper support to future versions of NAMDEnergy.


Marcelo Puiatti wrote:
> Dear users:
> Im a new user of NAMD. Ive AMBER parameter and topology files of
> organic ligands created with XLEAP tools. I know that I only need
> and NN.crd in order to run NAMD simulations with the keywords:
> amber on
> parmfile prmtop
> ambercoor inpcrd
> without a NN.psf file.
> My problem is that for the analysis of the output files, with VMD
> tools such as NAMD ENERGY, I need a psf file!! Can I make a psf file
> from and NN.crd files? Or I have to change my parameter files
> (*.dat, *.lib and frcmod) from AMBER format to CHARMM *.inp format.
> I could use PTRAJ tools in the analysis of the NN.dcd files but
> PTRAJ recongnize the old "binpos" format. Can NAMD write output files
> in this format?
> Thanks Marcelo

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