(no subject)

From: Marcelo Puiatti (marcelo.puiatti_at_gmail.com)
Date: Wed Dec 20 2006 - 12:30:55 CST

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 NN.top and
NN.crdin 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 NN.top 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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