Re: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR NH3 HC NH3
You need to provide a parameter file with defined parameters for a "NH3 HC
NH3" angle. Or if for some mysterious reason you can rationalize it, you
could delete that angle from your psf file... but I wouldn't recommend that.
Chris
--
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu Voice: 217-244-1733
http://www.ks.uiuc.edu/~char Fax: 217-244-6078
On Sat, Jun 20, 2009 at 12:59 PM, gurunath katagi <gurukatagi_at_gmail.com>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
>
> 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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: Wed Feb 29 2012 - 15:52:56 CST