Re: [AMBER] cpptraj selection mask syntax issue during clustering

From: Liao via AMBER <>
Date: Thu, 14 Jul 2022 23:10:20 -0500

I think I figured it out, because in the clustering I didn’t add a reference, therefore the distance based mask wasn’t working properly. Adding a reference frame fixed it. Great to know.

Sent from my iPhone

> On Jul 14, 2022, at 10:35 PM, Liao via AMBER <> wrote:
> Dear List,
> When performing clustering analysis with cpptraj, there seems to be a syntax issue, that the same selection when using cpptraj to strip and align trajectories, can't be recognized. Example below:
> dbscan minpoints 1 epsilon 0.8 sievetoframe \
> rms :529.ND1|:191.NZ|:528.CD|:97.NE2,OE1|:134<:12&@CA&:1-197 nofit \
> This gives an error, saying
> Error: Mask stack is not empty.
> Error: Could not set up mask ':529.ND1|:191.NZ|:528.CD|:97.NE2,OE1|:134<:12&@CA&:1-197' for topology complex.gas.prmtop
> Main problem is that the distance range selection cannot be combined with others. If I switch the order of the selection, it runs, just omitting all the atoms (there are 17 in total) after the first | , as below
> Mask [:134<:12&.CA&:1-197|:529.ND1|:191.NZ|:528.CD|:97.NE2,OE1] corresponds to 12 atoms.
> This behavior doesn't seem to exist when using cpptraj to strip and align, that the distance selection mask can be combined with other masks by the | with no issue. If I copy and paste the exact selection above it will work properly.
> I wonder if there's any way to get this right? Other than explicitly listing out every single residue in the distance range mask?
> Thanks!
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Received on Thu Aug 04 2022 - 13:34:20 PDT
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