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 Thu Nov 17 2022 - 13:00:03 PST
