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

From: Dr. Anselm Horn <>
Date: Wed, 31 Mar 2021 10:08:58 +0200

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.



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
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