AMBER Archive (2008)

Subject: Re: AMBER: Dihedral Angle Parameters

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Jun 26 2008 - 17:20:41 CDT

as far as I know it's allowed, but you need to be careful to test it.
we did that in an initial version for our protein backbone params, but
one issue was that they didn't work properly for D amino acids.
you also have to be careful with asymmetric generic dihedrals, which can
be complicated and cause problems. but fundamentally I don't know of
anything in the code that prohibits it- maybe others will.
good luck!
carlos

On Thu, Jun 26, 2008 at 6:07 PM, Ilyas Yildirim
<yildirim_at_pas.rochester.edu> wrote:
> Dear Carlos,
>
> Yes, I mean symmetry about 0. For instance the alfa-dihedral angle for the
> RNA is defined with the following parameters:
>
> OS-P -OS-CT 1 0.25 0.0 -3. JCC,7,(1986),230
> OS-P -OS-CT 1 1.20 0.0 2. gg&gt ene.631g*/mp2
>
> The E_torsion energy function for this dihedral is symmetric about 0. If I
> add another paramater list for this dihedral angle (with a non-zero
> phase), it can become asymetric. However, I am not sure if this is allowed
> in amber force field. Thanks.
>
> Best,
>
> On Thu, 26 Jun 2008, Carlos Simmerling wrote:
>
>> symmetric about what? if still a cosine term, then it has an intrinsic symmetry.
>> by varying phases, you can change symmetry about 0 if that's what you mean.
>>
>> On Thu, Jun 26, 2008 at 5:07 PM, Ilyas Yildirim
>> <yildirim_at_pas.rochester.edu> wrote:
>> > Dear AMBER users,
>> >
>> > I realized that the amber dihedral parameters are symmetric; the torsional
>> > energy vs angle has a symmetric character. Is it reasonable to create
>> > dihedral parameters for a particular dihedral angle such that it will have
>> > an asymmetric torsional energy function in amber force field? Thanks in
>> > advance.
>> >
>> > Best,
>> >
>> > --
>> > Ilyas Yildirim
>> > ---------------------------------------------------------------
>> > = Department of Physics - =
>> > = University of Rochester - =
>> > = 585-275-6766 (office) - 585-267-5644 (home) =
>> > = http://www.pas.rochester.edu/~yildirim/ =
>> > ---------------------------------------------------------------
>> >
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>
> --
> Ilyas Yildirim
> ---------------------------------------------------------------
> = Department of Physics - =
> = University of Rochester - =
> = 585-275-6766 (office) - 585-267-5644 (home) =
> = http://www.pas.rochester.edu/~yildirim/ =
> ---------------------------------------------------------------
>
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-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
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Stony Brook University E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
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