Hi,
I am a PhD student and I am pursuing the structure determination of a DNA duplex
dodecamer by NMR. I am comparing a DNA duplex containing a modified base,
in comparison to a control. I used antechamber and leap. Everything works great so far.
I also used MARDIGRAS to calibrate the NOEs, and use standard Watson-Crick hbonds to
keep the strands together. I used loose sugar angles based on J-coupling measurements.
I back-calculated my NOESY spectrum based on the calculated structure and it fits very well.
QUESTION #1:
I am using the following backbone dihedral angles typical for B-DNA (+/- 40 degrees):
(Bax et al., 1DUF.pdb)
$alpha = -61; $beta = 180; $gamma = 57;
$delta = 123; $epsi = -169; $zeta = -91;
Does this seem appropriate?
More importantly, how are the dihedral angles defined? Between -180 to +180? between -360 to +360?
Would -60 = 300 degrees?
If one look at
http://ambermd.org/tutorials/advanced/tutorial4/files/5col.bb
Is 2 CYT EPSILN -240.0 10.0 = -115 +/- 125 ?
QUESTION #2:
I used a very similar GB anneal protocol to the one describe by Ross Walker in one of his tutorial (see below).
I repeated the protocol 50 times using a different seed number to obtain a NMR ensemble,
and kept the 10 lowest energy (or 10 lowest rmsd) structures as representative ensemble.
I only have a few violations. e.g.:
Total distance penalty: 2.176
Total torsion penalty: 0.014
Does the protocol I am using here seems correct?
Should I do a minimization after? Or is this sufficient?
I would appreciate any comments.
Olivier
# simulated annealing protocol, 30 ps
&cntrl
nstlim=30000, pencut=-0.001, nmropt=1,
ntpr=200, ntt=1, ntwx=200, tempi=10,
cut=12.0, ntb=0, vlimit=10, rgbmax=12.0,
igb=1, saltcon=0.1, offset=0.13, ig=$seed
/
&ewald
/
#
#Simple simulated annealing algorithm:
#
#from steps 0 to 5000: heat the system to 600K
#from steps 5001-18000: re-cool to low temperatures with long tautp
#from steps 18001-20000: final cooling with short tautp
#
&wt type='TEMP0', istep1=0,istep2=5000,value1=600.,
value2=600., /
&wt type='TEMP0', istep1=5001, istep2=18000, value1=600.0,
value2=100.0, /
&wt type='TEMP0', istep1=18001, istep2=30000, value1=0.0,
value2=0.0, /
&wt type='TAUTP', istep1=0,istep2=5000,value1=0.4,
value2=0.4, /
&wt type='TAUTP', istep1=5001,istep2=18000,value1=4.0,
value2=4.0, /
&wt type='TAUTP', istep1=18001,istep2=19000,value1=1.0,
value2=1.0, /
&wt type='TAUTP', istep1=19001,istep2=30000,value1=0.1,
value2=0.05, /
&wt type='REST', istep1=0,istep2=3000,value1=0.1,
value2=1.0, /
&wt type='REST', istep1=3001,istep2=30000,value1=1.0,
value2=1.0, /
&wt type='END' /
LISTOUT=gb_$i.viol
DISANG=all.rst
/
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Received on Wed Oct 06 2010 - 11:00:03 PDT
