Re: [AMBER] Format of cpptraj pairwise distance file when clustering

From: Charo del Genio <>
Date: Tue, 4 Sep 2018 09:00:48 +0100

On 03/09/18 19:49, Daniel Roe wrote:
> Hi,
> What version of cpptraj are you using? Also, can you post your exact
> cpptraj input and output? The pairwise distance file format hasn't
> been ASCII in years - are you printing it out manually somehow?
> -Dan

Hi Dan,
        I'm using cpptraj from Ambertools18. In this specific instance, I start it with

cpptraj.OMP -p AFB5.prmtop -i

and the contents of are

trajin Production.mdcrd
cluster hieragglo epsilon 3.0 pairdist pairwisedistances.out savepairdist rms :70-74,336-340,369-374,394-402,429-434,453-458,478-482 mass summary cluster3.txt info cluster3info.txt repout cluster3rep

and the output file pairwisedistances.out is just as in my previous message.
Incidentally, I tried using the GitHub version of cpptraj, and the output is the same.



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Received on Tue Sep 04 2018 - 01:30:02 PDT
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