On Sun, Jul 22, 2012, Jio M wrote:
>
> I want to strip large number of residues (which are waters, > more than
> 20K that are not required).
You are correct in suspecting that there is a maximum line length in a
ptraj.in file.
Some ideas:
1. Use ranges to make the masks smaller: e.g. for the 1600's, use
strip 1600-1678,1680,1682,1686,1688,1692-1699.
2. Break things up into smaller strip commands, and do them in reverse order,
i.e. strip the largest residue numbers first, moving towards smaller ones.
That way, the residue renumbering problem will not come into play.
3. Maybe whatever analysis you want to do can proceed without stripping at
all(?)
4. Are you sure you want to keep the same water residues throughout the
trajectory? For example water 1687 (which you don't strip) may start out in
an interesting place (say near the active site, or whatever), but it will
quickly move somewhere else, and another water will take its place. So
keeping just a few waters based on the residue number may not be what you want
to do. There are commands to keep and strip waters based on geometric
criterion that may be more appropriate.
...good luck....dac
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Received on Sun Jul 22 2012 - 05:30:02 PDT
