Re: Using NAMD with NMR structure

From: Steve Chou (
Date: Mon Oct 24 2016 - 13:18:34 CDT

1. The hydrogen atoms in NMR structures are usually not accurate - there
are many/some mis-assigned NOEs for most NMR structures.
2. The names for hydrogen atoms (nomenclature) in NMR structures are
usually different from those in NAMD.
3. As for the protonation state, you can check the pH of the buffer used
for NMR spectrum acquisition, which can be found in the header of the RCSB
pdb file.
4. Nowadays, NMR structure calculations (Cyana, ARIA, Amber, X-plor and
CNS) are also based on restrained MD using the simulated annealing

Therefore, it's safe to remove all hydrogen atoms in the NMR structure, and
use NAMD to generate all the hydrogen atoms.

On Sun, Oct 23, 2016 at 6:55 AM, Peter Freddolino <>

> 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.
> Best,
> Peter
> > 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

Steven Chou

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