On Fri, Oct 27, 2017, Rana Rehan Khalid wrote:
>
> this error message showed when I load the pdb file in the tleap
> Loading PDB file: ./4iae.pdb
> -- residue 7: duplicate [ CA] atoms (total 2)
> -- residue 7: duplicate [ CB] atoms (total 2)
> -- residue 7: duplicate [ CD] atoms (total 2)
> -- residue 7: duplicate [ CE] atoms (total 2)
> -- residue 7: duplicate [ CG] atoms (total 2)
> -- residue 7: duplicate [ NZ] atoms (total 2)
This is not a error message: just a informational one, that LEaP is taking
the first alternate conformer in the PDB file, and ignoring the rest. This is
what the message is trying to say here:
>
> (Same-name atoms are handled by using the first
> occurrence and by ignoring the rest.
> Frequently duplicate atom names stem from alternate
> conformations in the PDB file.)
So, if you are happy with using the "A" alternate (most often the case)
then you should be fine. If you need something else, you will have to
hand-edit the PDB file select the coordinates you wish to use, and delete
the others.
...hope this helps....dad
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Received on Fri Oct 27 2017 - 12:30:03 PDT
