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
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Received on Fri Nov 04 2016 - 07:30:02 PDT
