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 - 10:30:02 PST
