Re: AMBER: Hydrogen bonding question

From: David A. Case <>
Date: Tue, 15 Mar 2005 07:23:30 -0800

On Tue, Mar 15, 2005, wrote:
> I am trying to simulate a single strand of an oligonucleotide.
> At this point I am assuming that the reason for this is that the hydrogen
> bonding is not restricted in distance and that leap just picks any
> nucleotide that is complimentary to the another nucleotide when making
> the prmtop file. This then would lead to unreasonable hydrogen-bonding.
> Is there some way that I can restrict the distance nucleotides have to be
> from each other to be involved in hydrogen-bonding?

The force field itself determines what groups will hydrogen bond with others,
primarily by electrostatic complementarity. If a hydrogen-bond donar and
acceptor pair come close in space, they will have a favorable interaction; if
they are not close, there will be little interaction.

If you wish to artifically enforce certain H-bonds (say watson-crick pairs),
you could add distance or angle restraints, as outlined in Section 5.9
of the Users' Manual.

....good luck...dac

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Received on Tue Mar 15 2005 - 15:53:00 PST
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