Is it one of the termini? It may be that one of the oxygens in your PDB is
not recognized (different name). The library files
($AMBERHOME/dat/leap/lib) tell you what atoms are expected in what
residues. By comparing the residues you find in those files
(all_amino94.lib, all_amino94nt.lib, all_amino94ct.lib), you should be able
to narrow down where that OXT is coming from.
Good luck!
Jason
2010/6/24 Catein Catherine <askamber23.hotmail.com>
>
> Thank you Jason,
>
>
>
> I found an addition OXT atom was added, where it is not necessary. What
> should I do?
>
>
>
> Best regards,
>
>
>
> Cat
>
>
>
>
>
>
>
> > Date: Thu, 24 Jun 2010 10:02:01 -0400
> > From: jason.swails.gmail.com
> > To: amber.ambermd.org
> > Subject: Re: [AMBER] Error encounter when running tutorial 4b when
> running xleap with AMBER 10 and AmberTools 1.2
> >
> > Hello,
> >
> > On Thu, Jun 24, 2010 at 9:57 AM, Catein Catherine <
> askamber23.hotmail.com>wrote:
> >
> > >
> > > Dear Prof. David,
> > >
> > > > complex = loadpdb 1FKO_trunc_sus.pdb
> > > Loading PDB file: ./1FKO_trunc_sus.pdb
> > > Added missing heavy atom: .R<CPRO 243>.A<OXT 15>
> > > Illegal CONECT record in pdb file
> > > Illegal CONECT record in pdb file
> > > Illegal CONECT record in pdb file
> > > Illegal CONECT record in pdb file
> > > Illegal CONECT record in pdb file
> > > Illegal CONECT record in pdb file
> > > Illegal CONECT record in pdb file
> > > Illegal CONECT record in pdb file
> > > Illegal CONECT record in pdb file
> > > Illegal CONECT record in pdb file
> > > total atoms in file: 2015
> > > Leap added 2024 missing atoms according to residue templates:
> > > 1 Heavy
> > > 2023 H / lone pairs
> > >
> >
> > There's no error message here. I would visualize the PDB in a
> visualization
> > program (i.e. VMD or pymol or something of the like), and see if any of
> the
> > connectivity looks wrong. This message just states that leap doesn't
> > understand or agree with the connectivity defined in the PDB. I would
> > suggest saving the topology file and closely looking at the resulting
> > prmtop/inpcrd files in your visualization program and see if any bonds
> that
> > should be there are missing (especially disulfide bonds. I'm not sure if
> > leap would recognize those in CONECT cards).
> >
> > Good luck!
> > Jason
> >
> >
> > >
> > >
> > > Is it a normal error message I should get when I follow the steps of
> > > tutorial 4b?
> > >
> > > Best regards,
> > >
> > > Cat
> > >
> > >
> > >
> > > _________________________________________________________________
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> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Jun 24 2010 - 10:00:05 PDT
