Re: Using NAMD with NMR structure

From: Pardis Tabaee (
Date: Mon Oct 24 2016 - 11:26:09 CDT

Unless it meant PDF, i.e. the document format, then it's ok to remove hydrogens and much easier.

From: <> on behalf of Pardis Tabaee <>
Sent: 24 October 2016 17:20
Subject: Re: namd-l: Using NAMD with NMR structure

I think the question was how to keep the hydrogens from the NMR and not to get rid of them, to compare PDFs.

From: Brian Radak <>
Sent: 24 October 2016 15:02
To:; Pardis Tabaee;
Subject: Re: namd-l: Using NAMD with NMR structure

Would it be horrible to have psfgen build the hydrogens instead? I would probably trust the protonation state assignments from NMR more than my intuition, but the internal coordinate construction will just be modified to the force field values anyway, so there isn't really much information there in terms of the positions (just my opinion).

I would just do something like this:

>> grep -v " H" NMR.pdb > psfgenInput.pdb

and then use the new pdb as input.


On 10/24/2016 06:13 AM, Pardis Tabaee wrote:

Did you rename the Hydrogens? Because the NAMD hydrogens have diferent 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

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 ...<><>
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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 <><> 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

Brian Radak
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Argonne National Laboratory
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