Should now be fixed in the GitHub version of cpptraj.
-Dan
On Tue, Sep 4, 2018 at 11:02 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> 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
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Sep 04 2018 - 12:30:02 PDT
