Hello again,
The correct pdb produced the same error as before:
We used a -nc of -4, and the following error appeared in sqm.out.
QMMM: ERROR!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: E = NaN DeltaE = NaN DeltaP = 0.0000E+00
QMMM: Smallest DeltaE = 0.1798+309 DeltaP = 0.1798+309 Step = 0
And the same error came out when editing the sqm.in using the -ek flag to
this:
qm_theory='AM1', grms_tol=0.0002, tight_p_conv=0, scfconv=1.d-8
We also tried it with a -nc -3, however, sqm did not run, due to the
following error in the sqm.out file:
QMMM: System specified with odd number of electrons ( 311)
QMMM: but odd spin ( 1). You most likely have the charge of
QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run
calculation
Any suggestions?
Thanks,
Erin
On Wed, Jul 13, 2011 at 11:03 AM, intra\sa175950 <stephane.abel.cea.fr>wrote:
> Yes, your pdb files must follow the Protein Data Bank file format rules
> described here
>
> http://www.wwpdb.org/documentation/format32/sect9.html
>
> HTH
>
> Stephane
>
> -----Message d'origine-----
> De : Erin Kelly [mailto:erkelly4572.gmail.com]
> Envoyé : mercredi 13 juillet 2011 17:57
> À : AMBER Mailing List
> Objet : Re: [AMBER] TR: Antechamber trouble with COA-acyl chain
>
> Thanks, I wasn't quite sure what was going on, what in particular was
> incorrect? I managed to fix mine just before you sent the formatted file,
> but I wasn't sure why. I just played around with spacing, is there a
> particular convention that always holds?
>
> Thanks again,
> Erin
>
> On Wed, Jul 13, 2011 at 10:34 AM, intra\sa175950
> <stephane.abel.cea.fr>wrote:
>
> > Hi Erin,
> >
> > Your pdb file was not in the PDB format (i.e. all the fields were not in
> > the good place). So I have reformatted it. Now your molecule is correct
> > RASMOL, VMD,...
> >
> > HTH
> >
> > Stephane
> >
> >
> > > -----Message d'origine-----
> > > De : Erin Kelly [mailto:erkelly4572.gmail.com]
> > > Envoyé : mercredi 13 juillet 2011 16:54
> > > À : AMBER Mailing List
> > > Objet : Re: [AMBER] Antechamber trouble with COA-acyl chain
> > >
> > > Dr. Case,
> > >
> > > I just noticed that the pdb coh1-1.pdb is flawed somehow, probably
> > because
> > > we added the numbers, so I'm going to send you the old coh1.pdb as
> well.
> > > I'll try to figure out why the coh1-1.pdb was unsuccessful.
> > >
> > > Thanks,
> > >
> > > Erin
> > >
> > > On Wed, Jul 13, 2011 at 9:28 AM, Erin Kelly <erkelly4572.gmail.com>
> > wrote:
> > >
> > > > Of course.
> > > >
> > > > Thanks,
> > > > Erin
> > > >
> > > >
> > > > On Wed, Jul 13, 2011 at 7:15 AM, David A Case
> > > <case.biomaps.rutgers.edu>wrote:
> > > >
> > > >> On Tue, Jul 12, 2011, Erin Kelly wrote:
> > > >> > Ok, so we edited the PDB to add unique atom names and changed the
> > > UNK.
> > > >>
> > > >> Can you post the final pdb file? (Note that the archive of old
> > > messages
> > > >> is
> > > >> always several days behind, so I can't try to reproduce the problem,
> > as
> > > I
> > > >> no
> > > >> longer have your input file, and it is not yet in the archive.)
> > > >>
> > > >> ...thx...dac
> > > >>
> > > >>
> > > >> _______________________________________________
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> > > >>
> > > >
> > > >
> >
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Received on Wed Jul 13 2011 - 11:00:04 PDT
