I did molecular dynamics simulations for different mutations and I want to compare how hydrogen bonds effects on stability and the other properties of mutations.
You may want to try the 'hbond' command in Cpptraj, freely available with AmberTools 14 (http://ambermd.org/AmberTools14-get.html). Cpptraj supports many popular MD trajectory formats.
Thanx alot dear # Luca Belmonte # Daniel R Roe for great answers but already i did the commands and measuring hydrogen bonds but my question about how to analyse if can guide me with a good references
Well it depends on what exactly you are looking for. The 'hbond' command should print a summary of what hbonds are present and statistics like how long etc. If you want to perform something like a hydrogen bond lifetime analysis you can use the 'lifetime' command in cpptraj. If you want secondary structure from hbond patterns you can use something like DSSP. Hopefully this helps, but if you are more specific about what you want/hope to learn I might be able to give a more detailed answer. See also http://www.ncbi.nlm.nih.gov/pubmed/21880522, which I have never used but you may find helpful.
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