Hi John,
The default criteria for HBOND in carnal is on p.224 of the Amber 7
manual. You may, however, specify the angle. Examples of the Hbond
command are on p. 232-233. Potential energy surface calculations for
inter- and intra-molecular hydrogen bonds have shown that the energies
depend more on the distance than the angle (until the angles are less
than 120 degrees), although both are important for hydrogen bonding to
occur.
Hope this helps.
Rhonda
On Mon, 29 Mar 2004, John wrote:
> Hello All,
>
> I would like to calculate potential hydrogen bonds in my structure. Using
> Carnal according to the manual the following command should be used:
> HBOND h1 DISTANCE 3.3 ANGLE ? STATS;
>
> Could you please tell me are the statistically preferred angles that Carnal
> uses as default? Is it a single set or is it a different set for specific
> hydrogen bonds under consideration? According to your experience is it
> better to use distances and angles when trying to investigate the
> statistical significance of hydrogen bond occurrence or only distances?
>
> Thank you for the help.
>
> Kind regards,
>
> John
>
>
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Received on Mon Mar 29 2004 - 19:53:00 PST
