From: sajad falsafi (
Date: Fri Oct 14 2011 - 08:06:08 CDT

Hi,   you should type this command in TkConsole for calculating H-bonds of water:    hbonds -sel1 [atomselect top "water"] * if sel1 and sel2 overlap, hbonds output is unreliable! also you can read all information about using the HBonds Plugin in this address: .   Sajad Falsafi & Zahra Karimi >________________________________ >From: subrata paul <> >To: >Sent: Friday, October 14, 2011 12:41 PM >Subject: vmd-l: hbond analysis > > >Dear Sir >I am a student of phd and new in VMD.When I went  through the VMD mailing list. > >I am using amber10. I loaded my trejectory and try to calculate but I could not.I think my command line is wrong. > >I want to calculate water-water  hbond. >measure hbonds 3.5 30 -sel1 [atomselect top "water"] -sel2 [atomselect top "water'] >Is this correct? >How to finde hbond/molecule > >Can you help me, giving me a example of hbond command line? > >Can you suggest me How can we do hbond vs time? > >Any help would be greatly appreciated! > >very very Thanking youSubrata Paul >IITGuwahati >India Assam > > > >