H-bond occupancy in nucleic acids

From: Tianjiao Wang (tjwang_at_iastate.edu)
Date: Thu Nov 20 2008 - 10:08:27 CST

Dear NAMD users,

  I have tried to calculate H-bond occupancy of my simulation (NAMD 2.6) of a
short nucleic acid using VMD1.8.6. If anyone has this kind of script, would
you share it with me. I appreciate your kind help.

  Alternatively, I have also found a h-bonds.tcl script that is developed by
Lu Dong to calculate H-bond occupancy in protein. The hbond.tcl is attached.
I typed "source bonds.tcl" in TK console in VMD to test a protein simulation
trajectory. The script didn't give an output. Did I do something wrong?
Also, could someone give advice how to modify it for nucleic acids

  Thank you very much!


Tianjiao Wang
3288 MBB
Iowa State Univ
Ames, IA 50010
e-mail: tjwang_at_iastate.edu
tel: 515-441-6417(cell)

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