From: J. Rui Rodrigues (jrui_at_ci.uc.pt)
Date: Fri Nov 28 2003 - 09:40:46 CST
Hi,
You have defined the segment based on your pdb file but you are not reading
coordinates. You should add
coordpdb PROTmods.pdb PROT
after applying patches. You should also verify if you need to define atom
aliases before reading coordinates. Check the manual at
http://www.ks.uiuc.edu/Research/namd/current/ug/node19.html
Rui Rodrigues
Hua Wong <wong_at_ebgm.jussieu.fr> escreveu:
> 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 |
> ----------------------------------------------------------
>
>
-- J. Rui Rodrigues Departamento de Química Faculdade de Ciências e Tecnologia Universidade de Coimbra 3004-535 Coimbra Portugal
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