AMBER Archive (2008)

Subject: RE: AMBER: about hydrogen bond in amber force field

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed May 21 2008 - 22:32:06 CDT

Hi Ying,

Ptraj will do this for you - although as a post processing of the trajectory
file.

See section 6 of http://www.ambermd.org/tutorials/basic/tutorial3/index.htm

This will monitor a whole range of bonds. If however, you only want to
monitor a single distance then you can again use ptraj or something like VMD
will also do this for you giving you bond distance vs time.

All the best
Ross

> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of WANG,YING
> Sent: Wednesday, May 21, 2008 7:25 PM
> To: amber_at_scripps.edu
> Subject: AMBER: about hydrogen bond in amber force field
>
> Hi, Dear AMbers,
> I know that glycam06 doesnot consider hydrogen bond but only use
> vdw and electrostatic to represent the long range force. My
> question is: if I want to monitor the hydrogen bond, how can I
> do?
> If any boday know, could you tell me?
> Thanks a lot!
>
>
> Ying
>
>
>
>
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