Hi,
On Tue, Jan 19, 2021 at 12:50 PM Daniel Fernández Remacha
<dnlfr1994.gmail.com> wrote:
>
> Hi, its still Ambertools 16 version.
Yeah, that's what I thought. Looking at the code, the issue you are
facing is something that was fixed back in 2017. The more recent
version should work much better for you (I hope).
-Dan
> I’ve 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,
> > > >
> > > >
> > > >
> > > > 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
> > > >
> > > >
> > > >
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Received on Tue Jan 19 2021 - 10:30:02 PST
