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
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Received on Thu Jun 24 2010 - 10:00:04 PDT
