Thank you Niel, I thought about that the problem might be due to too general atom types.
-----Original Message-----
From: Niel Henriksen [mailto:shireham.gmail.com]
Sent: Mittwoch, 16. Juli 2014 17:20
To: AMBER Mailing List
Subject: Re: [AMBER] RNA covalent bond angles
This is something that we are aware of, but perhaps it should be described in detail somewhere. Like Christina said, it's a problem from long ago. I believe the reason the parameters don't match experimentally derived values is due to limitations from using the same atom type for multiple different atoms. The "exact" solution would be to have a unique atom type for every atom in your molecule, but that's not practical. Until we do a rehaul of the RNA/DNA atom typing, these errors will show up when doing the PDB validation steps.
If I recall, there are some truly bad angles in the purine bases.
Best,
--Niel
On Wed, Jul 16, 2014 at 8:11 AM, Blatter Markus <blatter.mol.biol.ethz.ch>
wrote:
> Hi Christina,
>
> Thank you for your reply, In fact the deviations show up
> systematically in most of the nucleotides and models. I just showed
> one part of the reprted list. I will have alook at the reference you
> recommended to me. I guess I will then just live with this old values.
>
> Regards
> Markus
>
> -----Original Message-----
> From: Christina Bergonzo [mailto:cbergonzo.gmail.com]
> Sent: Mittwoch, 16. Juli 2014 16:44
> To: AMBER Mailing List
> Subject: Re: [AMBER] RNA covalent bond angles
>
> Hello,
>
> As far as I can tell, these angle parameters are a holdover from the
> Weiner et al. 1986 force field, and have never been updated. You can
> read about how the parameters were generated here:
>
> http://onlinelibrary.wiley.com/doi/10.1002/jcc.540070216/abstract
>
> Is there any reason these deviations aren't "real"? If there was a
> significant force field artifact, I'd expect it to show up in more
> than one CT-CT-CT / OS-CT-N* angle.
>
> -Christina
>
>
> On Wed, Jul 16, 2014 at 3:33 AM, Blatter Markus
> <blatter.mol.biol.ethz.ch>
> wrote:
>
> > In the validation report of pdb deposition I get the error of
> > covalent bond angles to be more than six std off. I refined my
> > solution structure using an simulated annealing protocol in implicit
> > water and using the ff12SB force field. As far as I can see the bond
> > angles are taken from parm99.dat file. Comparing the values for the
> > violated angels in the parm99.dat file with the dictionary angels
> > the PDB validation uses reveals a significant discrepancy.
> > Specifically I talk about the RNA bond angles O4'-C1'-N9 -- > type
> > OS-CT-N* --> 109.5 (PDB 108.5) and C3'-C2'-C1' --> type CT-CT-CT -->
> > 109.5 (PDB 101.5).
> > Where are these specific angles in the parm99.dat come from. Since
> > there is no literature mentioned in the parm99.dat file I searched
> > myself and found only a paper from 1996 (New Parameters for the
> > Refinement of Nucleic Acid-Containing Structures). In this
> > publication the angels agree with what PDB validation refers to. Can
> > someone explain me where the amber values come from and maybe why
> > they appear to
> be significantly off?
> >
> > Here a part of the output of the PDB validation
> >
> >
> > ==> Covalent Angle Values:
> > The overall RMS deviation for covalent angles relative to the
> > standard dictionary is 1.5 degrees.
> > The following table contains a list of the covalent bond angles
> > greater than 6 times standard deviation.
> >
> > Deviation Residue Chain Sequence Model
> > AT1 − AT2 − AT3 Bond Dictionary Standard
> > Name ID Number
> > Angle Value Deviation
> >
> >
> −−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−
> −−−−−−−−−−−−−−−−−−−−−−−−−−−−
> > 4.8 U B 3 1
> > C1’ − C2’ − C3’ 106.3 101.5 0.8 0.8
> > 4.4 A B 4 1
> N9
> > − C1’ − O4’ 112.9 108.5 0.7 0.7
> >
> > Thanks very much
> > Markus
> >
> > ===========================================
> > ETH Zurich
> > Dr. Markus Blatter
> > Institute of Molecular Biology & Biophysics Schafmattstrasse 30, HPP
> > L12
> > 8049 Zurich, Switzerland
> > phone +41 (0) 44 633 0721
> > email blatter.mol.biol.ethz.ch
> > web http://www.mol.biol.ethz.ch
> >
> > Private
> > Hochwachtstrasse 39
> > 8400 Winterthur
> > mobile +41 (0) 76 488 7078
> > ===========================================
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
>
> ----------------------------------------------------------------------
> -----------------
> Christina Bergonzo, PhD
> Postdoctoral Researcher
> Department of Medicinal Chemistry, University of Utah
> 30 South 2000 East, Rm. 201
> Salt Lake City, UT 84112-5820
> Office: L.S. Skaggs Pharmacy Research Institute, Rm.4290
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652 / Fax: (801) 585-6208
>
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Received on Wed Jul 16 2014 - 09:00:04 PDT
