On Fri, 2014-05-02 at 00:35 +0530, amin.imtech.res.in wrote:
>
> Thanks. I downloaded the project files and generated the mol2 and .off
> files. I loaded the .off file using loadoff. Now I can see FAD in the
> list. But when I load the pdb file of FAD, i get
>
> > fad = loadpdb FAD.pdb
> Loading PDB file: ./FAD.pdb
> Created a new atom named: P within residue: .R<B5 904>
> Created a new atom named: PA within residue: .R<B5 904>
[snip]
> Created a new atom named: N10 within residue: .R<B5 904>
> Added missing heavy atom: .R<B5 904>.A<N9 25>
> Added missing heavy atom: .R<POP 905>.A<O5A 1>
> Added missing heavy atom: .R<POP 905>.A<PA 2>
> Added missing heavy atom: .R<POP 905>.A<OA1 3>
> Added missing heavy atom: .R<POP 905>.A<OA2 4>
> Added missing heavy atom: .R<POP 905>.A<OP 5>
[snip]
> Added missing heavy atom: .R<B5 904>.A<N6 17>
> Added missing heavy atom: .R<B5 904>.A<N7 22>
> total atoms in file: 53
All of the atom names from the residue in FAD.pdb _must_ match the atom
names used for the same atoms in the OFF files you downloaded.
That's how leap is able to determine the appropriate atom types. You
will need to modify all of the atom names in the FAD residue in your PDB
file to match those stored in the OFF files.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu May 01 2014 - 12:30:03 PDT
