In case you want to use Python, we added back "mindist" in pytraj:
http://amber-md.github.io/pytraj/latest/analysis.html?highlight=mindist#pytraj.mindist
Hai
On Mon, Jan 2, 2017 at 2:33 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> hi,
>
> can you try to add keyword "mindist" to nativecontacts?
>
> You can see an example here: https://github.com/
> Amber-MD/cpptraj/blob/master/test/Test_NativeContacts/RunTest.sh#L18
>
> Hai
>
> On Mon, Jan 2, 2017 at 2:21 PM, Chris Neale <candrewn.gmail.com> wrote:
>
>> Dear Users:
>>
>> I see that there was once a cpptraj command called mindist, that would
>> return the minimum inter-atom distance between two selection masks.
>>
>> I am most familiar with the term "depreciated" in computer code meaning it
>> is not recommended, but can still be used (whereas something like
>> "removed"
>> might be used if the command was no longer available).
>>
>> However, I can not figure out how to use any depreciated commands in
>> cpptraj, which is my main question here. The amber16 manual does not turn
>> up anything about how to do this with a search for the word depreciated.
>>
>> I do see that the cpptraj executable recommends to use the nativecontacts
>> command. However, as far as I can tell this does not give minimum
>> distances
>> but, rather, the number of inter-group contacts within a specified cutoff.
>>
>> Thank you,
>> Chris.
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Mon Jan 02 2017 - 12:00:03 PST
