[AMBER] CHAMBER and CMAP difficulty

From: Brian Radak <brian.radak.accts.gmail.com>
Date: Wed, 18 Mar 2015 10:03:53 -0500

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):

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)?

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


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 - 08:30:03 PDT
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