Hi,
Have you tried actually visualizing the trajectory? Based on your
input I would expect all.mdcrd and wat10.mdcrd to be the same because
they both only have 10 water molecules. The reason for this is that
'trajout' always occurs at the end of all actions. I think what you
want for all.mdcrd is 'outtraj', which processes coordinates during
actions, e.g.
parm test.prmtop
trajin test.inpcrd
outtraj all.mdcrd
closest 10 :205.OG noimage oxygen outprefix wat10
trajout wat10.mdcrd
Hopefully that clears things up - if not let me know. Good luck,
-Dan
On Wed, Dec 5, 2012 at 1:22 PM, Marc van der Kamp
<marcvanderkamp.gmail.com> wrote:
> Dear all,
>
> I'm resending this, as I am afraid my message was blocked / held up
> due to the attached files.
> I can send the test.prmtop and test.inpcrd files off list.
>
> On 5 December 2012 17:52, Marc van der Kamp <marcvanderkamp.gmail.com> wrote:
>> Dear all,
>>
>> I am running the following (test) input in cpptraj, AT1.2 (with up to
>> patch 29 applied).
>>
>> $ cat test.in
>> parm test.prmtop
>> trajin test.inpcrd
>> trajout all.mdcrd
>> closest 10 :205.OG noimage oxygen outprefix wat10
>> trajout wat10.mdcrd
>>
>> I expected that the wat10.mdcrd trajectory would only have 10 waters,
>> but it has all the waters (i.e. it is exactly the same as all.mdcrd
>> when I diff the files). The modified prmtop does have only 10 water
>> molecules.
>> What is going wrong?
>> I have attached the input coordinates (1 frame) and prmtop here so the
>> problem can be replicated. (Although I'm not sure if they will get
>> through at the system is quite large)
>>
>> Thanks,
>> Marc
>>
>> $ ./patch_amber.py --patch-level
>> Latest patch applied to AmberTools12: 29
>> Latest patch applied to Amber12: 13
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Wed Dec 05 2012 - 13:00:02 PST
