Oh that worked great! I had heard tell of the "chamber" command in parmed
but could not find it in the documentation (bc I only have the Amber14
release manual duh).
Semi-related follow-up: If I want to compare energies between NAMD and
AMBER, do I need any special flags in mdin? Is 1-4 scaling automagically
switched to CHARMM values?
On Wed, Mar 18, 2015 at 10:14 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> 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?
> [http://parmed.github.io/ParmEd/html/parmed.html#chamber] 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
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Brian Radak
Postdoctoral Scholar
University of Chicago
Department of Biochemistry & Molecular Biology
Gordon Center for Integrative Science, W323A
929 E. 57th St.
Chicago, IL 60637-1454
Tel: 773/834-2812
e-mail: radak.uchicago.edu
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Received on Wed Mar 18 2015 - 08:30:06 PDT
