Dear Amberites,
We are please to announce the release of SIRAH 2.0, a complete coarse-grained force field for biomolecules, running native on AMBER 14+. It contains parameters for proteins, DNA, lipids (DMPC), ions and solvent. It's very easy to use, just map and go!
This release brings major improvements to the former protein model, including a reviewed set of bonded and non-bonded parameters to better describe the conformational landscape and hydrophilic/hydrophobic balance of the residues.
The average accuracy of SIRAH 2.0 on AMBER (~3A) is comparable to high-resolution cryo-EM experiments, with a performance of 2.6 microseconds/day for a protein of 108 residues on a GTX 1080.
The preprint version of the submitted manuscript is available at BioRxiv [
https://doi.org/10.1101/436774]
SIRAH 2.0 is freely available at [
http://www.sirahff.com] together with tutorials and FAQs.
The group is now working on expanding the library of lipids and metallic ions (to be released in a month or so). Sugars are also on the way...
Stay tuned,
Matias
------------------------------------
PhD.
Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay
[
http://pasteur.uy/en/laboratorios-eng/lsbm]
[
http://www.sirahff.com]
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Received on Thu Oct 11 2018 - 08:30:02 PDT
