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