Re: Minimisation error

From: Hua Wong (wong_at_ebgm.jussieu.fr)
Date: Fri Nov 28 2003 - 02:32:49 CST

Indeed, I have solve the charm++ error by adding paraTypeCharmm on
I also checked my pdb and found 0.000 everywhere as coordinate :(

I join a sample of the psfgen script I edited:
----------------------------------------------

topology top_all22_prot.inp

segment PROT {
pdb PROTmods.pdb
}

patch DISU PROT:51 PROT:276
patch DISU PROT:129 PROT:195

writepsf output/PROT.psf
writepdb output/PROT.pdb
-------------------------------
The system I study has no solvent nor heteroatoms....

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
> >
>
>

-- 
----------------------------------------------------------
| Wong Hua (Student)                                       |
| Equipe de Bioinformatique Genomique et Moleculaire       |
| INSERM U436 Universite ParisVII     _____________________|
| 2 place Jussieu case 7113          | Tel:None            |
| 75251 PARIS Cedex 05               | Fax:None            |
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