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
>
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--
---------------------------------------------------------------------------------------
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 - 08:30:02 PDT
