On Tue, Sep 15, 2015, ankita mehta wrote:
> I am trying to create topology and coordinate file for the pdb attached..
>
> It gives the warnings while reading the structure and when these warnings
> are ignored and toplogy and coordinate file is generated , structure is
> faulty ........
To expand on the previous answer: read the warnings carefully. If you in fact
have alternate conformers for residue 823 in your input pdb file, LEaP may be
doing what you want (selecting the first conformer).
>
> Warning: Atom names in each residue should be unique.
> (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.)
>
Since there weren't any other warnings (e.g. about missing heavy atoms), I'm
guessing(?) that you have alternate conformers in the input PDB file.
If that is correct, you will need to explain what you mean by the statement
"structure is faulty".
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 15 2015 - 12:00:03 PDT
