Re: Using the CHARMM36 forcefield with NAMD

From: Kenno Vanommeslaeghe (
Date: Wed Apr 23 2014 - 12:28:33 CDT

- I don't think NAMD itself can read topology (rtf) files
- You cannot use an old psf with the new parameter (prm) files; you'll
have to regenerate the psf (with psfgen, VMD, CHARMM-GUI,...) based on the
new topology (rtf) files
- In release 36, we made the CHARMM force field modular, with water being
in a separate stream file. Unfortunately, this modularity doesn't work in
NAMD. The recommended workaround is to use a NAMD-specific version of the
water stream file ( toppar_water_ions_namd.str ) *and* to *always* read
*all* parameter files, even if they're not needed for a given simulation.
- If the above doesn't solve your problem, please give more details. "NAMD
crashing" is exceedingly vague and makes me feel like I shouldn't help you.

On 04/23/2014 12:15 PM, Alex Utev (CMP) wrote:
> Hi,
> I've recently downloaded the CHARMM36 force field to use with NAMD. I believe the 2 main files
> are the "par_all36_prot.prm" file and the "top_all36_prot.rtf" file. Previously just adding the files using
> the parameters field seemed to work but with the new v36 files this seems to result in NAMD crashing.
> Any ideas what the issue is?
> Alex Utev

This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:20:45 CST