Hello Thomas,
first of all thank you very much for your response !
And now to your comments...
My original input trajectory "prod_BASE_NAME_REIMAGED.mdcrd" is
of course already reimaged by commands:
--------------------
center :1-204
image familiar
--------------------
where :1-204 are all receptor and ligand residues.
I added here:
http://physics.ujep.cz/~mmaly/AMBER/
one more picture with the last (400th) frame of my original input
trajectory
with water box. From this picture could be seen that imaging was done OK.
I also uploaded there this last frame as the RST file together with
original
PRMTOP file. If you could try to do what I wanted to achieve it would be
great !
If you have no time to try to play with my system, please let me at least
know
more in detail your version of this two step procedure.
Thank you very much in advance !
Best wishes,
Marek
Dne Mon, 09 May 2011 23:31:14 +0200 Thomas Cheatham III <tec3.utah.edu>
napsal/-a:
>
>> 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 - 16:30:02 PDT
