> I tried to achieve this by performing "closestwater" command in two
> consequent steps (using AmberTools 1.4).
>
> A) To find the closest 50 water molecules to my ligand molecules (:ANS).
>
> B) To choose from this 50 water molecules the closest 10 to surface
> groups of my receptor (:G4A,0GA)
I just tried this, albeit in a slightly different way, and it worked fine.
I need more information to specifically debug your problem however and
have some comments.
> #1
> Just to save last (400th) frame from the original trajectory with
> only 50 closest water molecules to my ligand molecules (:ANS)
> ---------------------------------------------------------------------------------
> trajin prod_BASE_NAME_REIMAGED.mdcrd 400 400 1
> trajout prod_BASE_NAME_REIMAGED_OUT1.mdcrd netcdf
> trajout prod_BASE_NAME_REIMAGED_OUT1.pdb pdb
> strip :Na+
> solvent byres :WAT
> closestwater 50 :ANS first noimage
Check the output carefully to make sure that the "solvent" is as you
expect. I would do the strip after the closestwater.
Note also, to make sure that there is solvent around the molecule of
interest, since you are not imaging, you likely want to image prior...
center :ANS mass origin
image origin center familiar
closestwater 50 :ANS first noimage
> #3
> To retain only 10 closest H2O molecules (from that previously chosen 50)
> to the surface groups (:G4A,0GA) of my
> receptor and save as PDB file.
> -----------------------------------------------------------
> trajin prod_BASE_NAME_REIMAGED_OUT1.mdcrd 1 1 1
> trajout prod_BASE_NAME_REIMAGED_OUT.pdb pdb
> solvent byres :WAT
> closestwater 10 :G4A,0GA first noimage
Here check the solvent carefully in the output; is what is selected a
match to what you expect? I assume you used a modified prmtop
that had only the solute of interest plus 50 waters? Are you sure this
is correct???
To avoid the prmtop in the second stage, you can start up ptraj with a PDB
file from step #2 instead of the prmtop...
ptraj pdb < closest10.in
--tec3
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Received on Mon May 09 2011 - 15:00:03 PDT
