Hi,
I'm not sure I have a complete answer to your question yet, but I do
have several recommendations. First, try upgrading to the latest
version of cpptraj (either by using the GitHub version
https://github.com/Amber-MD/cpptraj or the one from AmberTools 20).
There have been a lot of fixes and enhancements since 2016.
> autoimage
> strip :WAT
> strip :Na+
You can just use 1 strip command here, and use 'parmout' or
'outprefix' to write the corresponding stripped topology, e.g.:
strip :WAT,Na+ parmout ../top/mir_nowat.prmtop
this makes it so you don't have to use all the 'parmstrip' commands at the end.
Hope this helps,
-Dan
> rms fit :1-59
> trajout trajectories/full_prod.mdcrd
> trajout trajectories/full_prod.nc
> run
> clear all
> parm ../top/mir_solv.prmtop
> parmstrip :WAT
> parmstrip :Na+
> parmwrite out ../top/mir_nowat.prmtop
> run
> clear all
>
>
> -----Mensaje original-----
> De: Daniel Roe <daniel.r.roe.gmail.com>
> Enviado el: jueves, 14 de enero de 2021 16:52
> Para: AMBER Mailing List <amber.ambermd.org>
> Asunto: Re: [AMBER] Error while clustering on CPPTRAJ
>
> Hi,
>
> It would help if we had more information. To start, can you post your entire cpptraj input and the version of cpptraj you are using? Thanks.
>
> -Dan
>
> On Thu, Jan 14, 2021 at 8:03 AM <dnlfr1994.gmail.com> wrote:
> >
> > Hi,
> >
> >
> >
> > I’ve been doing some clustering tests on several trajectory files,
> > using the dbscan algorithm. As mentioned in the manual, I am running
> > the kdist option to choose appropriate epsilon and k values. In order
> > to speed up the process I have used the savepairdist and loadpairdist
> > commands. However, I am getting the following error with some
> > trajectories --> Error: Number of columns in file changes at line 100.
> >
> > I suspect the problem appears when loading the pairdist matrix file,
> > since the number of times this error shows up matches with the number
> > of times that my scripts loads the matrixfile.
> >
> > However, the final kdist plots (see figure below) seem to be OK.
> >
> >
> >
> > Does anyone know why this error is happening?
> >
> >
> >
> > By the way, the shape of the curves does not change much after kdist=4
> > (as explained in the user’s guide), but the height still varies
> > remarkably even with kdist=10. I am not sure if the epsilon and k
> > values of any of these tests can be used for the final clustering or more tests would be required.
> >
> >
> >
> > Any help is really appreciated.
> >
> >
> >
> > Daniel Fernández
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Jan 14 2021 - 16:00:02 PST
