AMBER Archive (2004)

Subject: Re: AMBER: H Bonds

From: anshul_at_imtech.res.in
Date: Thu May 06 2004 - 17:51:32 CDT

Dear Bill
Thanks for ur reply.
I think the suggeestion given by Sanjeev is more appropriate ie the angle
repoted by Carnal is H-D...A and not D-H...A.I also checked it with
insightII which gives the value for H-D...A as 17.69 (which is same as
reported by carnal) and for D-H...A as 151.63.I would also like to know if
there is some special reason for getting H-D...A in amber unlike the other softwares which report D-H...A.

With regards,
Anshul

On Wed, 5 May 2004, Bill Ross
wrote:

> > The other thing I want to ask is about the angle which is given in the
> > list file. The angle given by carnal is quite different from that given by
> > some other software. Can anyone through some light on this.
>
> The angle reported by carnal is as follows:
>
> D-H...A
>
> where D is donor, H is the hydrogen, and A is the acceptor - H
> is the apex point of the angle. Perhaps your other software uses
> a different atom as the apex?
>
> Also, if a series of angles is treated statistically (e.g. averaged),
> the correct way to do it is via 'circular statistics', and possibly
> your other software does not do this. (This method allows the average
> of 359 degrees and 1 degree to be 0 rather than 180.)
>
> Bill
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