I can confirm that the back mapping implemented by the sirah team works
well.
On Wed, Mar 31, 2021, 4:09 AM Dr. Anselm Horn <anselm.horn.fau.de> 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 www.sirahff.com, 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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Received on Wed Mar 31 2021 - 04:30:02 PDT
