Dr. Simmerling,
Thank you for the pointers. The initial single-stranded RNA form is coiled, but not A-form.
That is why I started from a wide energy well range (say -69.0 +/- 40' deg for the alpha),
but with the force constants no higher than the 32.0 shown in the sample input. I will focus on the
force specs first. For a stretch of 6 nts (all backbone angles) to which the etstraints were applied
the "RESTRAINTS" value reported in the out file varied approximately from 1.0 to 15.0.
Since I never used the dihedral restraints before, I am not sure if it's too high or too low.
Thank you again, Voytek Kasprzak
Wojciech (Voytek) Kasprzak (Contractor)
Analyst Programmer,
Basic Science Program,
Leidos Biomedical Research, Inc.
Frederick National Laboratory for Cancer Research (FNLCR)
Frederick, MD 21702
(301) 846 5537
http://binkley2.ncifcrf.gov/users/kasprzak
________________________________________
From: Carlos Simmerling [carlos.simmerling.gmail.com]
Sent: Friday, November 04, 2016 10:10 AM
To: AMBER Mailing List
Subject: Re: [AMBER] RNA backbone dihedral restraints question
I'm not clear on what you're doing. Do the restraint target values match
the initial structure? If not, how high are the initial energies? you might
also consider making the initial values match the input structure, then
changing the target values over time to match the desired structure. this
avoids the high penalties that can come with severe mismatch. also keep in
mind that the restraint force constants are in radians, so if you are
getting low penalty energies but it isn't matching your target values, you
might want to increase the force constants.
On Fri, Nov 4, 2016 at 10:05 AM, Kasprzak, Wojciech (NIH/NCI) [C] <
kasprzaw.mail.nih.gov> wrote:
> Dear Amber Users,
>
> I have been trying to temporarily force a single-stranded fragment of a
> larger RNA in
> a GB neck2 protocol simulation into a proper A-form (half) helix geometry
> using backbone
> dihedral angle restraints shown below (illustrated for only one
> nucleotide). I employed several
> different four point (r1 .. r4) ranges around the ideal A-form values (+/-
> 70' down to +/-2'
> illustrated below), but despite seeing that restraints are being used
> (non-zero values listed in
> in the MD output file), the actual angles measured by cpptraj dihedral
> command vary a lot, and
> the single stranded fragment turns from bad to worse (dramaticaly bending
> in all directions)
> in just 10 ns of MD simulation.
>
> Am I missing something fundamental in the restraints specifications? If
> the restraints are
> defined correctly, what else should I look for? Is there any
> other/simpler way to force a
> single-stranded RNA fragment into A-form backbone geometry?
> (If you need more data from me, please let me know)
>
> Sample backbone angle restraints for one RNA nucleotide (G4) employed in
> test runs:
>
> # 4 GUA ALPHA: (3 DA O3')-(4 DG P)-(4 DG O5')-(4 DG C5') -71.0 -67.0
> around -69.0 deg
> &rst iat = 96, 97, 100, 101,
> r1 = -72.0, r2 = -71.0, r3 = -67.0, r4 = -66.0,
> rk2 = 32.0, rk3 = 32.0,
> &end
> # 4 GUA BETA: (4 DG P)-(4 DG O5')-(4 DG C5')-(4 DG C4') 170.1 174.1
> around 172.1 deg
> &rst iat = 97, 100, 101, 104,
> r1 = 169.1, r2 = 170.1, r3 = 174.1, r4 = 175.1,
> &end
> # 4 GUA GAMMA: (4 DG O5')-(4 DG C5')-(4 DG C4')-(4 DG C3') 54.5 58.5
> around 56.5 deg
> &rst iat = 100, 101, 104, 124,
> r1 = 53.5, r2 = 54.5, r3 = 58.5, r4 = 59.5,
> &end
> # 4 GUA DELTA: (4 DG C5')-(4 DG C4')-(4 DG C3')-(4 DG O3') 80.8 84.8
> around 82.8 deg
> &rst iat = 101, 104, 124, 129,
> r1 = 79.8, r2 = 80.8, r3 = 84.8, r4 = 85.8,
> &end
> # 4 GUA EPSILN: (4 DG C4')-(4 DG C3')-(4 DG O3')-(5 DA P) -160.7
> -156.7 around -158.7 deg
> &rst iat = 104, 124, 129, 130,
> r1 = -161.7, r2 = -160.7, r3 = -156.7, r4 = -155.7,
> &end
> # 4 GUA CHI: (4 DG O4')-(4 DG C1')-(4 DG N9)-(4 DG C4) -73.8 -69.8
> around -71.8 deg
> &rst iat = 106, 107, 109, 123,
> r1 = -74.8, r2 = -73.8, r3 = -69.8, r4 = -68.8,
> &end
>
> Best regards, Voytek Kasprzak
>
>
> Wojciech (Voytek) Kasprzak (Contractor)
> Analyst Programmer,
> Basic Science Program,
> Leidos Biomedical Research, Inc.
> Frederick National Laboratory for Cancer Research (FNLCR)
> Frederick, MD 21702
> (301) 846 5537
> http://binkley2.ncifcrf.gov/users/kasprzak
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Nov 04 2016 - 08:00:03 PDT
