Dear Prof. Case,
Thanks for reply on Sunday :-)
>>2) i .e. strip the largest residue numbers first, moving towards smaller ones. That way, the residue renumbering problem will not come into play.
Thats very nice option, it never came in my mind (dull)
>> 4. Are you sure you want to keep the same water residues throughout the trajectory?
Actually I want to make a restart file and same residue number striping I will do in prmtop (using parmED, though not tried yet I will do after I strip waters in fast manner from inpcrd file).
This will be a periodic condition with side waters being removed. This I have been able to achieve playing/editing with pdb files, I just wanted to make things through amber modules to make things in "general".
>> There are commands to keep and strip waters based on geometric criterion that may be more appropriate.
Sorry I am not able to get, "strip waters based on geometric criterion". This may be really useful, like selective striping to make things periodic. Please some example.
thanks,
________________________________
From: case <case.biomaps.rutgers.edu>
To: Jio M <jiomm.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Sunday, July 22, 2012 5:46 PM
Subject: Re: [AMBER] stripping number of residues (>20K) problem
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 - 07:00:02 PDT
