yes, OPC is a 4-point water model.
On Fri, Nov 18, 2022 at 1:22 PM Kerry Woolnough via AMBER <amber.ambermd.org>
wrote:
> Hello David and Carlos,
>
> You are correct. The rst7 file is indeed a netCDF, and when that filetype
> is manually specified for VMD the rst7 and prmtop quickly load into a
> single molecule. Using ncdump, the netCDF says 22,609 atoms.
>
> From manual inspection of prmtop, it looks like each water molecule may be
> represented by 4 atoms (?), for example:
>
> H1 H2 EPW O H1 H2 EPW O H1 H2
> EPW O H1 H2 EPW O H1 H2 EPW O H1 H2 EPW O H1 H2 EPW O
> H1 H2
> EPW O H1 H2 EPW O H1 H2 EPW O H1 H2 EPW O H1 H2 EPW O
> H1 H2
> EPW O H1 H2 EPW O H1 H2 EPW O H1 H2 EPW O H1 H2 EPW O
> H1 H2
> EPW O H1 H2 EPW O H1 H2 EPW O H1 H2 EPW O H1 H2 EPW O
> H1 H2
> EPW O H1 H2 EPW O H1 H2 EPW O H1 H2 EPW O H1 H2 EPW O
> H1 H2
>
> Which could explain why the atoms aren’t tallying up as I expected. I’m
> guessing these are dummy atoms that were added by the water model?
>
> On a related note, what is meant by ‘residues’ in the context of
> solvateOct’s output?
>
> >solvateOct ramp OPCBOX 10.0
> Scaling up box by a factor of 1.362725 to meet diagonal
> cut criterion
> Solute vdw bounding box: 45.394 31.223
> 30.488
> Total bounding box for atom centers: 72.648 72.648
> 72.648
> (box expansion for 'iso' is 56.3%)
> Solvent unit box: 18.865 18.478
> 19.006
> Volume: 199737.607 A^3 (oct)
> Total mass 106080.564 amu, Density 0.882 g/cc
> Added 5341 residues.
>
> It does not seem to align with the number of solvent molecules in my
> prmtop/netCDF (note my PDB contained 17 water molecules before solvation…
> not sure if these are retained)
>
> Thanks again,
> K
>
> From: David A Case <david.case.rutgers.edu>
> Date: Thursday, November 17, 2022 at 3:47 PM
> To: Kerry Woolnough <woolnouk.uoguelph.ca>, AMBER Mailing List <
> amber.ambermd.org>
> Subject: Re: [AMBER] Restart and Topology Files Contain Different Numbers
> of Atoms
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>
> On Thu, Nov 17, 2022, Kerry Woolnough via AMBER wrote:
>
> >When I load rst7.pdb in VDM it says the file contains 17,289 atoms and
> >5320 water molecules. When I open the rst7 in cpptraj however, I’m told
> >it contains 22,609 atoms. In a text editor, rst7.pdb contains 22,610 atoms
> >(according to the atom number column) and the numbering of WAT atoms looks
> >a little weird… numbers are being skipped resulting in each WAT molecule
> >advancing the atom count by 4 instead of by 3 (as can be seen in the
> >snippet below). This makes me think the atom numbers are overestimating
> the
> >number of water molecules by 5320.
>
> By default, cpptraj does not output the "extra" points to a PDB file,
> which is
> why you see the missing numbers. You can use the "-ep" flag in ambpdb to
> override this behavior.
>
> I don't have any ideas about why VMD is hanging when you try to load a
> prmtop
> and rst7 file. Are you sure that your "rst7" file is indeed a formatted
> file,
> and not a netCDF file with a misleading name? If you type "head
> <prmtop-file>" and head <rst7-file> both should have a same number of
> atoms,
> reported as the first integer in the file.
>
> .....dac
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Received on Fri Nov 18 2022 - 10:30:03 PST
