Hi,
OK, I see what's happening here. You're forcing cpptraj to use the
ASCII pairwise distance file format by appending the '.out' extension.
As a temporary workaround use the binary pairwise distance file format
(via a '.cmatrix' extension, or by using the default file name) for
clustering; if you need the file in ASCII format as well just add a
'writedata' statement after all analyses have been run, for example:
parm parm.parm7
trajin traj.nc
cluster C1 :2-10 clusters 3 epsilon 4.0 out cnumvtime.dat summary
summary.dat savepairdist pairdist Cmatrix.cmatrix
run
writedata Cmatrix.out Cmatrix.cmatrix
I'll look into fixing the ASCII read/write issue in the meantime.
-Dan
On Tue, Sep 4, 2018 at 4:01 AM Charo del Genio <the.paraw.gmail.com> wrote:
>
> 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 cluster.in
>
>
> and the contents of cluster.in 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.
>
>
> Thanks,
>
> Charo
>
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Received on Tue Sep 04 2018 - 08:30:02 PDT
