[AMBER] Is there a bug in how Amber16 handles qmmask and WAT?

From: James Kress <jimkress_58.kressworks.org>
Date: Wed, 21 Feb 2018 16:25:25 -0500

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
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