Re: [AMBER] Restart and Topology Files Contain Different Numbers of Atoms

From: Kerry Woolnough via AMBER <amber.ambermd.org>
Date: Fri, 18 Nov 2022 18:21:57 +0000

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
CAUTION: This email originated from outside of the University of Guelph. Do not click links or open attachments unless you recognize the sender and know the content is safe. If in doubt, forward suspicious emails to IThelp.uoguelph.ca


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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Nov 18 2022 - 10:30:02 PST
Custom Search