From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Thu Jan 11 2007 - 20:13:41 CST
A parameter file is separate from the topology file (the NAMD
tutorial has pretty good descriptions of both at the end). In your
namd input file, you will need to source the correct parameter file;
probably the standard charmm par_all27_prot_lipid.inp will work.
On Jan 11, 2007, at 7:37 PM, Alexander Vaughn wrote:
> 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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