Actually , residue 823 is the GDP ..AS There are three chains in the
structure so there are three GDPs in the Pdb file...they are rsidue 823 ,
824 and 825... Problem is leap is recognizing one of them only ...when i
generate the structure from topology and inpcrd there is only one
gdp.......so i said structure is faulty.....tell me the way out how should
i rename them i mean where should i do this.............so that leap
recognizes all three differently......
thnks in advance!
On Wed, Sep 16, 2015 at 12:01 AM, David A Case <david.case.rutgers.edu>
wrote:
> 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
>
>
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Received on Wed Sep 16 2015 - 03:30:03 PDT
