Re: [AMBER] unable to find mopac charges

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 5 Oct 2012 07:59:54 -0400

Where did you get your PDB file? The PDB file specification is *very*
particular about what information belongs in which column of the file.
 There was 1 too many spaces between the atom name and the residue name,
and 2 too few spaces between the chain ID (A) and the residue number (1).
 This caused the atomic coordinates to be in an unexpected place (i.e.,
they were shifted 1 character too far to the left), so they were not parsed
correctly. As a result, antechamber assigned the coordinates of every atom
to be 0, 0, 0.

Here is a link to the PDB spec:
http://deposit.rcsb.org/adit/docs/pdb_atom_format.html

I have attached a 'fixed' version of the PDB file which works with
AmberTools 12 (I highly suggest upgrading to AT 12).

HTH,
Jason

On Fri, Oct 5, 2012 at 2:55 AM, Anogna <anognal.gmail.com> wrote:

> I am attaching my ligand pdb can u plz help me with this.
>
> On Wed, Oct 3, 2012 at 5:28 PM, David A Case <case.biomaps.rutgers.edu
> >wrote:
>
> > On Wed, Oct 03, 2012, Anogna wrote:
> > >
> > > When I tried to use antechamber to generate preparation file for
> > > my complex protein (the complex pdb structure is attached in the
> email),
> > I
> > > got
> > > an error message indicating "unable to find mopac charges in
> mopac.out".
> > > I check the test case and found no problem at all.
> > >
> > > The command i used:
> > > *antechamber -i lgn_h.pdb -fi pdb -o lgn.mol2 -fo mol2 -c bcc -nc 1 -j
> 5*
> > > mopac.out file is also attached with this mail.
> > >
> > > And anyone can provide some solutions for me? Thanks!!
> >
> > How about just looking at what is in the mopac.out file??
> >
> > ...dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> ...........INDIA is great
>
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>


-- 
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032



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Received on Fri Oct 05 2012 - 05:30:03 PDT
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