From: Marcelo Puiatti (marcelo.puiatti_at_gmail.com)
Date: Wed Dec 20 2006 - 12:30:55 CST
I´m a new user of NAMD. I´ve 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:
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
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:17 CST