Re: how to caculate the hydrogen bonds occupancy?

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Sun May 13 2007 - 13:43:57 CDT

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measure hbonds

http://www.ks.uiuc.edu/Research/vmd/current/ug/node124.html

Regards,

      Gianluca

On Sun, 13 May 2007, lnubiofox wrote:

> Dear users, I want to analysis the hydrogen bonds of a dcd file,
> unfortunately as far as I know there is no tools which can do this
> containing in vmd. At first ,I try to use gromacs instead,however,after
> I am familiar with it I found that gromacs cannot read dcd files and it
> is impossible to get the tpr file which gromacs needed to analysis. Is
> there any scripts which help us to get the occupancy of hydrogen bonds
> during the simulation ? Or is there any other ways to achieve this using
> vmd ? Any suggestions will be appreciated. Best regards, Yuan Liu
> Liaoning university P.R.China

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