On Sun, Jul 22, 2012 at 9:46 AM, Jio M <jiomm.yahoo.com> wrote:
> 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).
>
ParmEd will also print out a stripped restart/inpcrd file if you want it to
(but only in the text-based version parmed.py, not xparmed.py). You need
to use "loadRestrt" first, then it will print out a matching inpcrd file
based on what strip commands you've used.
> 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.
>
Suppose there is a conserved water molecule in a specific site of the
protein (often the active site), and you want to observe the behavior of
this water molecule. If this is water #1 in the first frame, it is almost
certain that eventually water 1 will move out of that site and another
water (say #10) will move in. If you always keep water #1, you are NOT
always keeping the structurally important water bound at the interesting
site.
There are other commands (e.g., closest) that will keep water molecules
based on where they are in space -- that is, you can keep water molecules
based on their location rather than an arbitrary index. In this sense, it
is a 'geometric criteria' for water stripping rather than an index criteria.
I encourage you to play around with the different commands in ptraj, it's a
good way to learn what each is doing.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sun Jul 22 2012 - 11:30:02 PDT
