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 - 07:30:03 PDT
