Hello again,
it seems that problem was connected with usage of NETCDF format.
If I use RST or ASCI MDCRD format to save my intermediate product ( system
with 50 closest waters to ANS molecules)
then also second step B) is OK and I obtain desired final result.
On the other hand if I use as the container for my intermediate MDCRD in
NETCDF format (as I originally did), the second step (B) is
unsuccessful.
I uploaded here:
http://physics.ujep.cz/~mmaly/AMBER/
final fig SUCCESS.tiff as well as intermediate PRMTOP file (
With50ClosestWaters.prmtop ) to allow you
easily verify what I am saying.
It seems that routine "closestwater" might have in some cases problem with
NETCDF format,
at least speaking about AmberTools 1.4.
Best wishes,
Marek
Dne Tue, 10 May 2011 01:13:33 +0200 Marek Maly <marek.maly.ujep.cz>
napsal/-a:
> 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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>>
>
>
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Received on Mon May 09 2011 - 18:30:02 PDT
