Hi,
Try removing all whitespace from your mask string.
-Dan
On Thu, Feb 22, 2018 at 2:58 PM, James Kress <jimkress_58.kressworks.org> 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.
>
> 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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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Thu Feb 22 2018 - 12:30:03 PST
