From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sun Jun 21 2009 - 12:54:51 CDT
On Sat, 2009-06-20 at 23:29 +0530, gurunath katagi wrote:
> 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
please check your .psf file.
this looks as if you have an incorrect angle definition,
which could happen, if you have incorrect bonds.
> 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
-- ======================================================================= Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot.
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