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 - 13:30:03 PDT
