Re: [AMBER] Error while clustering on CPPTRAJ

From: Daniel FernŠndez Remacha <dnlfr1994.gmail.com>
Date: Tue, 19 Jan 2021 17:50:24 +0000

Hi, its still Ambertools 16 version.
Iíve already asked our cluster administrator to install Amber20 but I will have to wait a bit until I can test it with the latest version.

Daniel

________________________________
De: Daniel Roe <daniel.r.roe.gmail.com>
Enviado: Tuesday, January 19, 2021 6:39:31 PM
Para: AMBER Mailing List <amber.ambermd.org>
Asunto: Re: [AMBER] Error while clustering on CPPTRAJ

Hi,

On Tue, Jan 19, 2021 at 12:21 PM <dnlfr1994.gmail.com> wrote:
> I've been doing some more quicker tests using "sieve 10" and I found the following error in the pair-distance matrix file:

Just to clarify, is this with the AmberTools 16 version of cpptraj or
a more recent one?

-Dan

> #F1 F2 CpptrajPairDist
> 1 11 1.2672
> 1 21 1.7326
> 1 31 1.8467
> 1 41 2.3464
> 1 51 2.6885
> 1 61 3.2762
> 1 71 3.2343
> 1 81 3.1948
> 1 91 3.0762
> 1101 3.1559
> 1111 2.9725
> 1121 2.9481
> 1131 2.8394
> 1141 3.2183
> 1151 2.9452
> 1161 2.7912
> 1171 2.2689
> As you see, there is no separation between the first two columns from line 11 and below. It is the direct output of the matrixfile from cpptraj.
> Now the error line says: Error: Number of columns in file changes at line 11. So this is where Cpptraj fails to read the pair-distance matrix file.
>
> -----Mensaje original-----
> De: Daniel Roe <daniel.r.roe.gmail.com>
> Enviado el: viernes, 15 de enero de 2021 0:59
> Para: AMBER Mailing List <amber.ambermd.org>
> Asunto: Re: [AMBER] Error while clustering on CPPTRAJ
>
> 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 <mailto:daniel.r.roe.gmail.com> Enviado el: jueves, 14 de
> > enero de 2021 16:52
> > Para: AMBER Mailing List <mailto: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 <mailto:dnlfr1994.gmail.com> wrote:
> > >
> > > Hi,
> > >
> > >
> > >
> > > Iíve 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 userís 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 FernŠndez
> > >
> > >
> > >
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Received on Tue Jan 19 2021 - 10:00:03 PST
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