Addendum to Re: Minimisation error

From: Hua Wong (wong_at_ebgm.jussieu.fr)
Date: Fri Nov 28 2003 - 02:36:02 CST

Here is the log I obtain from the script:
----------------------------------------
PSFGEN from NAMD 2.5 for Linux-i686
reading topology file top_all22_prot.inp

>>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<
>>>>>>>>>>>>>>>>>>>>>>> July 1997 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<
>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<<

Created by CHARMM version 22 1
building segment PROT
reading residues from pdb file PROTmods.pdb
extracted 336 residues from pdb file
Info: generating structure...
Info: skipping improper N-C-CA-HN at beginning of segment.
Info: skipping conformation C-N-CA-C at beginning of segment.
Info: skipping conformation C-CA-N-HN at beginning of segment.
Info: skipping bond C-N at end of segment.
Info: skipping improper C-CA-N-O at end of segment.
Info: skipping conformation CA-C-N-CA at end of segment.
Info: skipping conformation N-CA-C-O at end of segment.
Info: skipping conformation N-CA-C-N at end of segment.
Info: segment complete.
applying patch DISU to 2 residues
applying patch DISU to 2 residues
Info: guessing coordinates for 5055 atoms (2509 non-hydrogen)
Warning: failed to guess coordinates for 5055 atoms
Info: writing psf file output/PROT.psf
total of 5055 atoms
total of 5126 bonds
total of 9311 angles
total of 13665 dihedrals
total of 818 impropers
Info: psf file complete.
Info: writing pdb file output/PROT.pdb
Info: pdb file complete.

----------------------------------------
Hope it helps you more than me

Thanks
Wong Hua

On Thu, 27 Nov 2003, Brian Bennion wrote:

> hello
>
> Did you solve your previous problem with the charm++ error?
> Because you have two atoms sitting on top of each other. Are there entries
> further up in the log file suggesting that atom coordinates are not
> unique? I suspect that you have at least two atoms with 0.000 0.000 0.000
> coordinates in your pdb file that was created by psfgen....
>
> Brian
>
>
> On Thu, 27 Nov 2003, Hua Wong wrote:
>
> > Is there a value I have to check especially for this kind of case?
> >
> > TCL: Minimizing for 400 steps
> > ETITLE: TS BOND ANGLE DIHED
> > IMPRP ELECT VDW BOUNDARY MISC
> > KINETIC TOTAL TEMP TOTAL2 TOTAL3
> > TEMPAVG
> >
> > ENERGY: 0 2685892.8098 -99999999.9999 -99999999.9999
> > -99999999.9999 -515429.7900 99999999.9999 0.0000
> > 0.0000 0.0000 -99999999.9999 0.0000 -99999999.9999
> > -99999999.9999 0.0000
> >
> > INITIAL STEP: 1e-06
> > GRADIENT TOLERANCE: nan
> >
> > Thanks
> >
> > Wong Hua
> >
>
>

-- 
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| Wong Hua (Student)                                       |
| Equipe de Bioinformatique Genomique et Moleculaire       |
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