Re: Using NAMD with NMR structure

From: Peter Freddolino (
Date: Sun Oct 23 2016 - 05:55:08 CDT

The hydrogens should not be the problem as long as they follow the naming scheme specified by the topology file, but on the other hand, their positions are mostly determined by the heavy atoms and they relax very quickly during MD, so there is not much to be gained by keeping the NMR hydrogens (although I would recommend using that information to assign protonations states, especially to histidines, since it is available).
To get more help than that, you’d need to provide more detail on the ‘ugly error’ that you’re seeing.


> On Oct 23, 2016, at 3:00 AM, Oscar Bastidas <> wrote:
> Hello,
> 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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