that makes sense. Thanks!
On Tue, Jun 11, 2013 at 4:22 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Tue, Jun 11, 2013 at 4:13 PM, Jonathan Gough
> <jonathan.d.gough.gmail.com>wrote:
>
> > I'm asking as I want to confirm that I have created a solvent box
> (TIP4PEW)
> > with the correct # of ions to give a desired ion concentration.
> >
> > Leap tells me, when I solvate it has added 26249 residues.
> > The prmtop file (NRES) says that it contains 26852 residues
> >
> > that tracks with the protein size.
> >
> > However - when we use ambpdb to write a pdb file, we only see ~6249 water
> > molecules.
> >
> > The number of water residue labels (in the prmtop) also matches the
> number
> > from leap and the prmtop.
> >
> > Visualization of the inpcrd/prmtop and the pdb shows that they are the
> same
> > size and they directly overlap.
> >
> > is leap/prmtop simply counting every atom of TIP4PEW as a residue?
> >
>
> No, it's a bit more mundane. The PDB file only permits 4 digits for the
> residue number, so the numbering 'cycles' every 10K residue numbers.
>
> Ergo, the residue number in the PDB is the real residue number % 10000,
> which seems to be what you're seeing.
>
> This is one of the chief weaknesses of the PDB file format.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Tue Jun 11 2013 - 14:00:03 PDT
