Hydrogen bond detection and shape complementarity

[Anonymous]

HI,

I have PDB strucures of antigen- antibody complexs. want to studythe hydrogen bond pattern at the ineterface and also the shape complimentarity. As per the following manuscript (Kuroda et al, (2016) Bioinformatics, 32(16):2451-2456) the command line

report_hbonds_for _plugin.linuxgccrelease

-s

-prevent packing true

sc.linuxgccrelease

however the command is not functioning in my rosetta installation.i can run other command line for docking but not the above mentioned command. Please any one let me know its precise location in the rosetta folder so that i can set env path in the ~/.BASHRC FILE.

Anticipating a response soon

Suji george

National institute of Virology,

Pune, india

 

[Anonymous]

It looks like both of these apps are pilot apps, and should have been moved to public apps upon publication.  I’ll open a PR to move these into public apps and they will be in the next weekly release of Rosetta.

[Anonymous]

Thank you very much for the prompt response

regards 

Suji George 

[Anonymous]

 

 Hi,

I have found  an alternative to the above mentioned  report_hbonds_for _plugin.linuxgccrelease and sc.linuxgccrelease. The Interfaceanalyser does the job of reporting the shape complimentarity and hydrogen bond parameters. The interfaceanalyser also reports the pymol selection of the residues. However is there a way to get detailed output report of the residue and atom involved in the hydrogen bond, something similar to the program HBPLUS. As per the following manuscript (Kuroda et al, (2016) Bioinformatics, 32(16):2451-2456)  the results from the HBPLUS and report_hbonds_for _plugin.linuxgccrelease are similar. Similarly is it possible with Interfaceanalyser to report the residue and atom involved in the hydrogen bond of the interface of the complex. 

With Regards

Dr. Suji george 

[Author]

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