FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE

From: Alexander Vaughn (aevaughn_at_gmail.com)
Date: Thu Jan 11 2007 - 19:37:34 CST

This is the outpute of trying to run a namd2 minimization calculation from 3
different pdb files(one protein, one water, and one the residue), and using
one topology file that has information for all three parts. The psfgen
program ran without any errors, the namd2 program however does have a fatal
error as seen below.
Thanks in advance for your assistance!

Charm++: standalone mode (not using charmrun)
Info: NAMD 2.6 for Linux-i686
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
Info:
....
Info: 1 NAMD 2.6 Linux-i686 1 ubuntumachine aevaughn
Info: Running on 1 processors.
Info: 7244 kB of memory in use.
Info: Memory usage based on mallinfo
Info: Configuration file is 2LBD.conf
TCL: Suspending until startup complete.
...
Info: COORDINATE PDB ./2LBDpro.pdb ./2LBDwat.pdb ./2LBDret.pdb
Info: STRUCTURE FILE ./2LBD.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS ./top_retacid.inp
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE ./top_retacid.inp
LINE=*MASS 1 H 1.00800 H ! polar H*
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE
./top_retacid.inp
LINE=*MASS 1 H 1.00800 H ! polar H*

Stack Traceback:
....
Charm++ fatal error:
FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE ./top_retacid.inp
LINE=*MASS 1 H 1.00800 H ! polar H*

-- 
Alex Vaughn
aevaughn_at_uab.edu

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