Re: [AMBER] CHAMBER and CMAP difficulty

From: Jason Swails <>
Date: Wed, 18 Mar 2015 11:14:29 -0400

On Wed, 2015-03-18 at 10:03 -0500, Brian Radak wrote:
> I've been happy to see a lot of recent activity in CHAMBER development.
> However, I'm still having trouble building parm7/rst7 combinations from
> XPLOR PSF/PDB pairs built with NAMD/PSFGEN and CHARMM36 with CMAP.
> I built a simple dipeptide in vacuum and put it through CHAMBER with both
> the "-nocmap" and "-cmap" flags, but only the former completes without
> errors and yields output. In the latter case I get the somewhat cryptic
> message (also with "-verbose" on):

Does the 'chamber' action in the Github version of ParmEd work?
[] chamber is
getting replaced with that in the upcoming release, and ParmEd seems to
have fewer issues reading files than chamber (and also has some smarter
defaults, and supports things like NBFIX that chamber does not).

> Checking for flag: CMAP
> Examining potential match: PSF
> Examining potential match: CMAP
> CMAP Found
> Found 1 unique cmap types:
> Type: 1 - 3 5 7 3 5 7 3 5
> C NH1 CT1 C NH1 CT1 C NH1
> ERROR end of file for reading CMAP
> Is this a problem reading the PSF or the PAR file (with the CMAP spline)?

Looks like a problem parsing the PAR file. chamber expected more lines
than it had.

> I *believe* I took this version of CHAMBER from the Amber14 development
> version back in September, so it looks up-to-date. The prm/rtf files are
> from CHARMM-GUI (the *de facto* standard for most CHARMM FF builds these
> days). I also tried the above with a PSF built by CHARMM but with the same
> error.

Are they truncated? Again, I've never had trouble with ParmEd (and
CHARMM-GUI is actually going to start using ParmEd internally to provide
Amber inputs shortly, alongside CHARMM, NAMD, Gromacs, and OpenMM input,
I believe).

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Wed Mar 18 2015 - 08:30:04 PDT
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