ptraj will also do this:
----------------------------------------------------------------
trajin mdcrd
(or "trajin restrt_file restart" if it's a restart file).
strip :WAT
trajout pdb_file pdb
----------------------------------------------------------------
Then load the PDB file into leap. rdparm can strip waters and write
out a new parmtop, but it is an old format that can't be used with
sander/pmemd.
Good luck!
Jason
On Wed, Feb 24, 2010 at 12:34 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>> I would like to unsolvate already solvated=2C EM-zed protein.
>
> Easiest way I know is
>
> % egrep -v WAT solvated.pdb > unsolvated.pdb
>
> This removes all lines containing WAT. If you want to get rid of
> ions too, and your ion is Na,
>
> % egrep -v 'WAT|Na' solvated.pdb > unsolvated.pdb
>
>> I am thinking to do it in xleap=2C but don't know how.
>
> xleap is not designed for it.. manual deletion of each water
> is the only way I know.
>
> Bill
>
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>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Feb 23 2010 - 22:00:03 PST
