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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Received on Wed Dec 05 2012 - 12:30:02 PST
