FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR NH3 HC NH3

From: gurunath katagi (gurukatagi_at_gmail.com)
Date: Sat Jun 20 2009 - 12:59:51 CDT

Hello everyone,
I have a PDB file glob1.pdb..(file generated by combining two pdb files). I
have created the psf file using the script .
I need to minimize the structure using namd.
when I run the file as:
/home/dynamics/NAMD_2.6_Linux-i686/namd2 ghb_minimize.conf >ghb.log , the
following error is generated:

------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR NH3 HC NH3

Charm++ fatal error:
FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR NH3 HC NH3
Aborted
My question is : whether I have to alter the psf file that i have got.. or
give a parmater file for heme since C-CPB bond is found in the psf file.

The files can be downloaded from the following link:

http://ssl.serc.iisc.ernet.in/~pralay/Pralay%27s%20Home_files/publication/minimize_hb.tar.gz

protein.pdb -- the original pdb file
protein_1.pdb -- the pdb file created by psfgen
protein_1.psf -- the psf file creted after psfgen
deoxy_psf.tcl -- script for psf file cretation
minimize.conf -- config file for minimization

The topology and parameter file that i have used include --
top_all27_prot_lipid.inp , toppar_all22_prot_heme.str,
top_all27_prot_lipid_gsh.inp and par_all27_prot_lipid.inp

Can any body please look into this.and give some suggestions.

-- 
Gurunath M Katagi
M.Sc (engg) Research student
Supercomputer Education and Research Centre
Indian Institute Of Science
Bangalore

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