See section 6 of tutorial B3 :
http://ambermd.org/tutorials/basic/tutorial3/section6.htm
It should be fairly easy for you to modify the donor / acceptor definitions
for your system.
Good luck,
Ross
> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> Behalf Of workalemahu berhanu
> Sent: Sunday, August 16, 2009 1:13 PM
> To: AMBER Mailing List
> Subject: [AMBER] Variations of the number of total hydrogen bond in MD
> simulations using ptraj
>
> Dear amber users
> I would like to analysis my trajectory file for the change in the
> total number of hydrogen bonds in my peptide and peptide with ligand
> which is having beta sheet secondary structure in MD simulation. Is it
> possible to do it using ptraj? Could anyone provide me a script for
> this kind of analysis?
> Thank you
> With regards
>
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Received on Wed Aug 19 2009 - 23:13:58 PDT
