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.
This is confirmed by using:
qmmask=':5-7,16-18 | (:5-7,16-18 <:9.0 & :Na+)',
which recovers the residues and Na+ found with ambmask
Also, if I try
qmmask=':5-7,16-18 | (:5-7,16-18 <:5.0 & :WAT)',
I get the residues and all the WATs
And when I do
qmmask='(:5-7,16-18 <:5.0 & :WAT)',
I just get all the WATs with no residues
I've looked through the mailing list archives and have seen this problem
reported previously. However, I could not find any solution in the
archives.
Any ideas why Amber16 has these problems with qmmask and WAT?
Thanks.
Jim Kress
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Received on Wed Feb 21 2018 - 13:30:02 PST
