I'm not familiar with that work or what the goal of their
restraints was, so I can't really help any more. You can use dihedral
restraints in Amber, you can find examples in the archive by
searching for "dihedral restraint" or perhaps "DISANG".
There is a section in the Amber9 manual at page 178.
we might be able to help more if you can give specific questions
about things that are unclear.
On 9/14/07, Hu, Shaowen (JSC-SK)[USRA] <Shaowen.Hu-1.nasa.gov> wrote:
>
> re-post my reply.
>
> -----Original Message-----
> From: Hu, Shaowen (JSC-SK)[USRA]
> Sent: Friday, September 14, 2007 12:32 PM
> To:
> 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,
> Shaowen
>
> Thanks Carlos. I am testing some simulation annealing method by using
> the restraint files provided by
> http://amber.scripps.edu/tutorial/dna_NMR/nmr_dna_tutorial.htm
>
> 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,
> Shaowen
>
>
> -----Original Message-----
> From: owner-amber.scripps.edu on behalf of Carlos Simmerling
> Sent: Fri 9/14/2007 11:00 AM
> To: amber.scripps.edu
> 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] <Shaowen.Hu-1.nasa.gov> 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
> >
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Sep 16 2007 - 06:07:39 PDT
