From: Pardis Tabaee (pardis.tabaee.d_at_hotmail.co.uk)
Date: Mon Oct 24 2016 - 06:13:04 CDT
Did you rename the Hydrogens? Because the NAMD hydrogens have different labels ("names"). E.g. maybe in your NMR software like crystallographic softwares, you have H1 or H2, but in NAMD you'll have something like this http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node24.html
Usually when you simply include the topology file that should be it, but it can happen that psfgen doesn't recognise the labels, so you must have a quick look and fix them yourself, or try an alternative topology file.
Topology Files - Theoretical and Computational Biophysics ...<http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node24.html>
Parameter Files Up: NAMD Tutorial Previous: PSF Files. Topology Files A CHARMM forcefield topology file contains all of the information needed to convert a list of ...
> On Oct 23, 2016, at 3:00 AM, Oscar Bastidas <bastidasoh_at_mymail.vcu.edu> wrote:
> 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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