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 - 01:30:02 PDT
