[AMBER] cpptraj selection mask syntax issue during clustering

From: Liao via AMBER <amber.ambermd.org>
Date: Fri, 15 Jul 2022 11:35:23 +0800

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?

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Received on Thu Aug 04 2022 - 13:34:19 PDT
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