From: gurunath katagi (gurukatagi_at_gmail.com)
Date: Sun Jun 21 2009 - 16:35:42 CDT
as you pointed out, there are few incorrect angle and bond definitions.
basically, there is a bond between atom no. 2314, 2315 , 2316, 2317 which
are repeated twice in the bond information section. a part of psf file is
pasted here:
2311 K 147 HEME CGD CC 0.620000 12.0110 0
2312 K 147 HEME O1D OC -0.760000 15.9990 0
2313 K 147 HEME O2D OC -0.760000 15.9990 0
*2314 E 1 GGL N NH3 -0.300000 14.0070 0*
2315 E 1 GGL HT1 HC 0.330000 1.0080 0
2316 E 1 GGL HT2 HC 0.330000 1.0080 0
2317 E 1 GGL HT3 HC 0.330000 1.0080 0
2318 E 1 GGL CA CT1 0.210000 12.0110 0
2319 E 1 GGL HA HB 0.100000 1.0080 0
2320 E 1 GGL C CC 0.340000 12.0110 0
2308 2310 2311 2312 2311 2313 2315 2314
2315 2314 2316 2314 2316 2314 2317 2314
2317 2314 2318 2314 2318 2319 2318 2320
On Sun, Jun 21, 2009 at 11:24 PM, Axel Kohlmeyer <
akohlmey_at_cmm.chem.upenn.edu> wrote:
> 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.
>
> cheers,
> axel.
>
> > 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
>
> --
> =======================================================================
> 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.
>
>
-- Gurunath M Katagi M.Sc (engg) Research student Supercomputer Education and Research Centre Indian Institute Of Science Bangalore
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