Using NAMD with NMR structure

From: Oscar Bastidas (
Date: Sun Oct 23 2016 - 02:00:14 CDT


I want to use one model from a NMR ensemble for a MD simulation, but unlike
crystal structures, the NMR model has hydrogens. I'm trying to follow
through the tutorial PDF for NAMD but when I get to the step of creating
the psf file manually for my protein, I get an error message saying the the
topology file cannot be opened and that the molecule has been destroyed by
a fatal error. I make the .pgn file as instructed in the tutorial, but
when I try to run psfgen in the TK window, I get that ugly error. My hunch
is that the hydrogens in the NMR model may be the source of my trouble
since the tutorial is geared at placing hydrogens where none exist in a
.pdb file.

Any help with running NAMD on a NMR model would be helpful. Thank you.

Oscar Bastidas, Graduate Student
Department of Chemical and Life Science Engineering
Virginia Commonwealth University

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