From: Marcelo Puiatti (marcelo.puiatti_at_gmail.com)
Date: Wed Dec 20 2006 - 12:30:55 CST
Dear users:
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:
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?
Thank´s Marcelo
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:17 CST