Re: [AMBER] Convert SIRAH coarse-grained model back to all-atomic pdb file format?

From: Matias Machado <>
Date: Wed, 31 Mar 2021 12:26:05 -0300 (UYT)

Dear Michael,

Making a specific tutorial for SIRAH Tools is in my veeeery long list of "To-do" things...

As Anselm and Carlos mentioned, the backmaping capabilities of SIRAH are implemented through the VMD plugin "sirah_vmdtk.tcl".

As stated in every SIRAH tutorial, once you load the topology and trajectory file in VMD (e.g. "vmd your.prmtop -e sirah_vmdtk.tcl") you can access the functionalities of the plugin by executing the following command in the Tcl/Tk console of VMD:


Particularly the command you are looking for is:

 sirah_help sirah_backmap

Note, backmaping requires AMBER Tools 14+ for minimazing the reconstructed coordinates, it can also profit from the MPI code.

I also strongly recommend to use de default options for minimization, which render the best results in terms of convergence and speed.
Be aware that not always increasing the minimization steps is the best choce, that is conditioned by the minimization options and the starting point of the coordinates.

The simplest way to try the command is by executing:

 sirah_backmap now

which will backmap the actual frame you are placed at in the trajectory (otherwise it will start backmapping the whole trajectory, which may be time consuming).

Best regards,


Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay

----- Mensaje original -----
De: "Carlos Simmerling" <>
Para: "AMBER Mailing List" <>
Enviados: Miércoles, 31 de Marzo 2021 8:00:48
Asunto: Re: [AMBER] Convert SIRAH coarse-grained model back to all-atomic pdb file format?

I can confirm that the back mapping implemented by the sirah team works

On Wed, Mar 31, 2021, 4:09 AM Dr. Anselm Horn <> wrote:

> Dear Michael,
> although I have not used SIRAH by now, I had read in the documentation
> that backmapping is already implemented via a VMD script, as stated in:
> Machado & Pantano 2016 (DOI 10.1093/bioinformatics/btw020)
> The authors refer to the website, where under
> "Download" -> "Sirah for Amber" a tgz-archive is available, within which
> the tcl-script sirah_vmtk.tcl is provided in the tools subdirectory.
> Maybe you could use vmd in the non-graphical scripted mode to perform
> backmapping from the command line.
> Regards,
> Anselm
> On 03/31/2021 09:39 AM, Charo del Genio wrote:
> > On 31/03/2021 07:39, Michael Shokhen wrote:
> >> Dear AMBER experts,
> >> The coarse-grained SIRAH force field is implemented in AMBER20.
> >> There are several tutorials also. Thanks to them I have converted
> >> PDB all-atomic structure of my protein to the SIRAH coarse-grained
> >> file format and successfully conducted molecular dynamics simulation.
> >> The problem is how to convert the final SIRAH coarse-grained
> >> file format of my protein back to all-atomic PDB file format.
> >> Unfortunately, this information is missed in AMBER SIRAH tutorials.
> >> Your help appreciated.
> >> Michael
> >
> > Dear Michael,
> > I have written a C code that backmaps SIRAH CG structures into FG
> ones, and I plan to publish it as part of a work that is still in progress.
> How urgently do you need the backmapping done?
> >
> >
> > Cheers,
> >
> > Charo
> >
> >
> >
> >
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