[AMBER] Post_analysis_Amber_tools_suggestion

From: Antonio Amber Carlesso <antonio.amber.carlesso.gmail.com>
Date: Sun, 18 Nov 2018 15:09:51 +0100

Hi all,

By reading these two interesting articles, I am wondering if similar
analysis are manageable using Amber tools as well..

https://www.ncbi.nlm.nih.gov/pubmed/28319010

https://www.ncbi.nlm.nih.gov/pubmed/27019343



We are interested for example in investigate through time evolution of the
MD the electrostatic, “hydrophobic” interaction and number of contacts
between a series of protein-protein molecular object..


And do you believe is more “efficient” dealing with PBC “issues” directly
with GROMACs or even the PBC re-imaging should be fixed with Ambertools?



Thank you for your possible suggestions!


[image: analysis.PNG]

Figure. (D) Peptide-target recognition map.(E and F) Dynamic electrostatic
interaction energy, on the peptide and protein side, respectively.





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analysis.PNG
(image/png attachment: analysis.PNG)

Received on Sun Nov 18 2018 - 06:30:04 PST
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