On Wed, Feb 21, 2018, James Kress wrote:
> As I have reported previously, ambmask and qmmask give different results for
> identical inpcrd, prmtop, and mask inputs.
>
> ambmask
>
> ambmask -p prmtop -c inpcrd -find ':5-7,16-18 | (:5-7,16-18
> <:5.0 & :WAT) | (:5-7,16-18 <:9.0 & :Na+)'
>
> I get 379 atoms selected. I get 6 Na+, 176 WAT (44 water
> molecules), and the balance are the DNA residues.
>
> qmmask
>
> qmmask=':5-7,16-18 | (:5-7,16-18 <:5.0 & :WAT) | (:5-7,16-18
> <:9.0 & :Na+)',
>
> Yields 17964, atoms where all the additional atoms (in
> excess of the 379 found by ambmask) are from all the WATs being included.
What happens with qmmask='(:5-7,16-18 <:5.0)'? Do you get all the Na+?
All the WAT's?
The qmmask code is calling the same underlying code as ambmask. But maybe
the water positions are not correctly identified when qmmask is invoked.
Or maybe the qm code is doing something funny with WAT residues.
I know this is no solution. But it looks like we would need a real example
to trace down a number of possible problems.
....dac
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Received on Tue Feb 27 2018 - 18:00:03 PST
