AMBER Archive (2005)

Subject: Re: AMBER: Hydrogen bonding question

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Tue Mar 15 2005 - 09:21:37 CST

opitz_at_che.udel.edu wrote:

>Dear Amber Community,
>
>I am trying to simulate a single strand of an oligonucleotide. This
>results in a the strand folding onto itself in implicit solvent.
>Then I tried to place it in explicit solvent and equilibrate the pressure
>to 1 bar. Then I removed the restraints from the molecule and let it
>move. Agin, this resulted in the strand folding onto itself.
>
>
>
do you have reason to think that this is not correct?

>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.
>
>
I don't quite understand you - Leap does not pick things for hydrogen
bonds, these
are just determined by the interaction between atoms in your system.
Leap does not
choose any that are preferred.

>Is there some way that I can restrict the distance nucleotides have to be
>from each other to be involved in hydrogen-bonding?
>
>
do you mean the distance in space, or in sequence? if space, there
really is no way
to modify it unless you decide to make a new force field. if sequence,
then you
are putting restrictions on what structures can form- you can do this
with distance
restrained but you should only do this if you have a very good reason
(such as
experimental data). if your simulation is not matching the experiment,
adding
restraints might fix it but you have to wonder why it is not matching,
and perhaps other
things will not match either. This may be a sign that this is not a good
model for
the system you are studying.

>Furthermore, is there some way to do this in the sander input file? I am
>asking this, because I am running Amber on a cluster, in which I do not
>have any access to the basic amber code. I have it on my workstation, but
>when running large scale simulations I do not have access to the sander code.
>
>
>
yes, read the section of the manual on restraints in Sander.

>Best Regards,
>
>Armin
>
>
>
>
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