So 6.18.1 is a version before the ‘changenames’ keyword was added. Your
best bet is to install the GitHub version of cpptraj:
https://github.com/Amber-MD/cpptraj
Hope this helps,
-Dan
On Sat, Oct 12, 2024 at 9:21 AM Maciej Spiegel <maciej.spiegel.umw.edu.pl>
wrote:
> Hi,
>
> CPPTRAJ v6.18.1),
>
> This was one installed along with the AmberTools23 *via* Conda
>
> conda install -c conda-forge ambertools=23
>
>
> Maciej Spiegel, MPharm PhD
> *assistant professor*
>
> *Department of Organic Chemistry **and **Pharmaceutical Technology,*
> *Faculty of Pharmacy, **Wroclaw Medical University*
> *Borowska 211A,
> <https://www.google.com/maps/search/Borowska+211A,+50-556+Wroclaw,+Poland?entry=gmail&source=g> **50-556
> Wroclaw, Poland
> <https://www.google.com/maps/search/Borowska+211A,+50-556+Wroclaw,+Poland?entry=gmail&source=g>*
>
> Wiadomość napisana przez Daniel Roe <daniel.r.roe.gmail.com> w dniu 12
> paź 2024, o godz. 15:10:
>
>
>
> Hi,
>
> What version of cpptraj are you using? The ‘changenames’ keyword was
> introduced in 6.22.2.
>
> -Dan
>
> On Sat, Oct 12, 2024 at 4:40 AM Maciej Spiegel via AMBER <
> amber.ambermd.org> wrote:
>
>> Hello,
>>
>> I am following this tutorial:
>> https://amberhub.chpc.utah.edu/create-new-nucleotide-for-amber/ <
>> https://amberhub.chpc.utah.edu/create-new-nucleotide-for-amber/> , but
>> when I reach the step:
>>
>> > atommap o37-with-charges.mol2 o37-for-charges.pdb mapout atommap.dat
>> changenames
>> or
>> > strip .C17,1H17,2H17,3H17 charge -1.0
>>
>> I encounter errors:
>>
>> < Error: [atommap] Not all arguments handled: [ changenames ]
>> and
>> < Error: [strip] Not all arguments handled: [ charge -1.0 ]
>> respectively.
>>
>> I thought the issue was due to using an old version of AmberTools, but I
>> updated to the latest version (CPPTRAJ v6.18.1), and the problem still
>> persists.
>> Any thoughts?
>> –
>> Maciej Spiegel, MPharm PhD
>> assistant professor
>> .GitHub <https://farmaceut.github.io/>
>>
>> Department of Organic Chemistry and Pharmaceutical Technology,
>> Faculty of Pharmacy, Wroclaw Medical University
>> Borowska 211A, 50-556 Wroclaw, Poland
>> <https://www.google.com/maps/search/Borowska+211A,+50-556+Wroclaw,+Poland?entry=gmail&source=g>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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Received on Sat Oct 12 2024 - 08:00:02 PDT
