RE: AMBER: DNA base planarity restraint

From: Hu, Shaowen (JSC-SK)[USRA] <"Hu,>
Date: Fri, 14 Sep 2007 13:29:13 -0500

 re-post my reply.

-----Original Message-----
From: Hu, Shaowen (JSC-SK)[USRA]
Sent: Friday, September 14, 2007 12:32 PM
Subject: RE: AMBER: DNA base planarity restraint

Thanks Carlos. My previous reply may have been evaporated since I did
not receive it. Can I get to know how to use improper dihedrals
restraint with AMBER?


Thanks Carlos. I am testing some simulation annealing method by using
the restraint files provided by

To modify the distance restraint to my system is very cubersome and I
can not understand well why each restraint is posed. Other people (some
HADDOCK works) used base planarity combined with WC, sugar pucker and
phosphate backbone dihedral restraints, and got good results. Their
restraints looks more intuitive to me.

Thanks again,

-----Original Message-----
From: on behalf of Carlos Simmerling
Sent: Fri 9/14/2007 11:00 AM
Subject: Re: AMBER: DNA base planarity restraint
can you tell us first why you think that you need it?
you can use improper dihedrals but don't do this unless you are very
sure that the existing force field is not correct for your project.

On 9/14/07, Hu, Shaowen (JSC-SK)[USRA] <> wrote:
> Dear all,
> Could anybody kindly tell how to apply planarity restraint to DNA
> bases? I could not find one in Manual or mail list archive.
> Thanks a lot,
> Shaowen

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Received on Sun Sep 16 2007 - 06:07:38 PDT
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