Hi,
Thank you for answering that fast.
I am not sure of how to check the cpptraj version. It is the included with AMBER16. Running with cpptraj.cuda
The input is the following:
parm ../top/mir_nowat.prmtop
trajin trajectories/full_prod.mdcrd
cluster c1 dbscan kdist 1 rms :1-59&!.H= savepairdist pairdist matrixfile
cluster c2 dbscan kdist 2 rms :1-59&!.H= loadpairdist pairdist matrixfile
cluster c3 dbscan kdist 3 rms :1-59&!.H= loadpairdist pairdist matrixfile
cluster c4 dbscan kdist 4 rms :1-59&!.H= loadpairdist pairdist matrixfile
cluster c5 dbscan kdist 5 rms :1-59&!.H= loadpairdist pairdist matrixfile
cluster c6 dbscan kdist 6 rms :1-59&!.H= loadpairdist pairdist matrixfile
cluster c7 dbscan kdist 7 rms :1-59&!.H= loadpairdist pairdist matrixfile
cluster c8 dbscan kdist 8 rms :1-59&!.H= loadpairdist pairdist matrixfile
cluster c9 dbscan kdist 9 rms :1-59&!.H= loadpairdist pairdist matrixfile
cluster c10 dbscan kdist 10 rms :1-59&!.H= loadpairdist pairdist matrixfile
The mdcrd file is previously aligned using this other input. So it combines 3 trajectories (300ns total).
parm ../top/mir_solv.prmtop
trajin ../mdcrd/mir01prod.nc
trajin ../mdcrd/mir02prod.nc
trajin ../mdcrd/mir03prod.nc
autoimage
strip :WAT
strip :Na+
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
>
>
>
> _______________________________________________
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> AMBER.ambermd.org
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Received on Thu Jan 14 2021 - 10:00:02 PST
