Re: about hydrogen bond analysis

From: Mo Chen (
Date: Tue Mar 24 2015 - 16:19:37 CDT

You do not need to define DONOR and ACCEPTOR in the topology files BEFORE
the simulations. You can do the analysis in VMD by either using the plugin
at Extension->Analysis->Hydrogen Bond, or running a tcl script from
terminal or Tk console.


On Tue, Mar 24, 2015 at 2:07 PM, Hasan haska <>

> Dear All,
> I’m planning to do a hydrogen bond analysis for the atoms in different
> molecules that can generate hydrogen bonds. So, do I have to define DONOR
> and ACCEPTOR terms in their topology files before starting the simulations
> ? or anything that I must do for the preparation ? And Are there any tools
> or packages you suggest me about this analysis ?
> Thanks.

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