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
> > >>
> > >>
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >
> > >
>
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>
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Received on Wed Jul 13 2011 - 09:30:04 PDT
