Hi Alejandro,
The script to get the RMSD plot is different
for example: you must create this file in a text editor (your_script).
trajin equil.mdcrd.gz 1 250 1 # this your trajectory file(s)
reference ras-raf_solvated.inpcrd # this your complex.inpcrd file
rms reference out equil.rmsd .CA,C,N # the equil.rmsd will be your output.
Then, you should run the script: $ ptraj your_solv_complex.prmtop your_script
Thus, you should use the equil.rmsd as input for xmgrace.
Best,
Aldo
=======================================
Aldo Segura-Cabrera
Postdoctoral Fellow
Division of Experimental Hematology and Cancer Biology
Cancer and Blood Diseases Institute
Cincinnati Children's Hospital Medical Center
3333 Burnet Ave, MLC 7013, Cincinnati OH 45229
e-mail: Aldo.Segura-Cabrera.cchmc.org; aldosegura.gmail.com
=========================================
El Jueves, 20 de febrero, 2014 11:29:12, Javier Alejandro Rendon Carrillo <biotecnologo.rendon.gmail.com> escribió:
Hi Aldo!
That means
that after run the production in the AMBER MMPBSA
tutorial<
http://ambermd.org/tutorials/advanced/tutorial3/section2.htm>
,
output files from the production (run.x) prod1.out, prod2.out prod3.out and
prod4.out
can be ploted without been processed by perl?
2014-02-20 9:35 GMT-06:00 Aldo Segura <asegurac666.yahoo.com.mx>:
> Hi Alejandro,
>
> Those scripts just will produce the two column files, then you can use
> them as input for xmgrace or gnuplot to get the plots.
>
>
> Best,
>
> Aldo
>
>
> =======================================
> Aldo Segura-Cabrera
> Postdoctoral Fellow
> Division of Experimental Hematology and Cancer Biology
> Cancer and
Blood Diseases Institute
> Cincinnati Children's Hospital Medical Center
> 3333 Burnet Ave, MLC 7013, Cincinnati OH 45229
> e-mail: Aldo.Segura-Cabrera.cchmc.org; aldosegura.gmail.com
> =========================================
>
>
>
> El Jueves, 20 de febrero, 2014 10:13:04, Javier Alejandro Rendon Carrillo <
> biotecnologo.rendon.gmail.com> escribió:
>
> Hi DAC!
>
> I´ve working in the MMPBSA.py method using a DNA-Protein complex, im
> following this tutorial
> http://ambermd.org/tutorials/advanced/tutorial3/section2.htm , now i have
> a
> question after execute the pruduction
> run.x how i get the plots of the the
> density<
> http://ambermd.org/tutorials/advanced/tutorial3/files/prod_summary.DENSITY
> >
> , temperature<
> http://ambermd.org/tutorials/advanced/tutorial3/files/prod_summary.TEMP>
> , total energy<
> http://ambermd.org/tutorials/advanced/tutorial3/files/prod_summary.ETOT>
> and
> backbone RMSD<
> http://ambermd.org/tutorials/advanced/tutorial3/files/measure_prod_rmsd.ptraj
> >
> .
> should i use the same command line used before ./process_mdout.pl heat.out
> density.out equil.out
> what is the command line need to get the plots?
>
> greetings!
>
>
>
>
>
>
> --
>
>
> LBG Javier Alejandro Rendón Carrillo
> Laboratorio de Investigación y Desarrollo
>
> Tel. (044) 81-80-52-05-76
>
>
>
> El control del espacio y el estricto manejo
> del tiempo son factores determinantes
> para aquellas personas que pretendan
> alcanzar y sostener un desempeño
>
eficiente.
> CONTROL DEL ESPACIO: Orden en las
> cosas, en los archivos y en los registros.
> ESTRICTO MANEJO DEL TIEMPO: Ser
> puntual y saber fijar prioridades y
> cantidades de tiempo
> M. Kant
> Año-1780
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
LBG Javier Alejandro
Rendón Carrillo
Laboratorio de Investigación y Desarrollo
Tel. (044) 81-80-52-05-76
El control del espacio y el estricto manejo
del tiempo son factores determinantes
para aquellas personas que pretendan
alcanzar y sostener un desempeño
eficiente.
CONTROL DEL ESPACIO: Orden en las
cosas, en los archivos y en los registros.
ESTRICTO MANEJO DEL TIEMPO: Ser
puntual y saber fijar prioridades y
cantidades de tiempo
M. Kant
Año-1780
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 20 2014 - 09:00:03 PST
