Hi,
Thanks Dan, you were right.
Marc
On 5 December 2012 20:52, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed Dec 05 2012 - 14:00:02 PST
