I am trying to use AMBER 10 to fit RDC data to fixed coordinates but
am having a problem with a "No restraint defined" message. Any help
would really be appreciated!
My input control file is:
&cntrl
nmropt=2, igb=0, imin=1, maxcyc=500, ncyc=40, ntpr=20,
ntb=0, cut = 15, iscale = 5, ntt = 1, vlimit = 30,
/
&ewald
eedmeth=5,
/
&wt type='END' /
LISTOUT=POUT
DIPOLE=RST.dip
And the header of my RDC data file is:
# RDC data
&align
freezemol=.true., ndip=44, dij=44*1.08, gigj=44*7.84089,
dwt=44*0.3, dcut=-1.0,
s11=0.000, s12=0.000, s13=0.000, s22=0.000, s23=0.000,
id(1)=12, jd(1)=13, dobsl(1)= 11.02, dobsu(1)= 15.02,
id(2)=46, jd(2)=47, dobsl(2)= 10.35, dobsu(2)= 14.35,
id(3)=43, jd(3)=44, dobsl(3)= -18.72, dobsu(3)= -14.72,
id(4)=80, jd(4)=81, dobsl(4)= 18.05, dobsu(4)= 22.05,
id(5)=123, jd(5)=124, dobsl(5)= 28.52, dobsu(5)= 32.52,
id(6)=147, jd(6)=148, dobsl(6)= 16.14, dobsu(6)= 20.14,
Even though the RDC is not defined my output file does somehow list my
RDC data in the final results but without fitting it:
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 0.000 ps
Begin reading energy term weight changes/NMR restraints
WEIGHT CHANGES:
** No weight changes given **
RESTRAINTS:
Requested file redirections:
LISTOUT = POUT
DIPOLE = RST.dip
** No restraint defined **
Done reading weight changes/NMR restraints
Alignment info will be read from file: RST.dip
Here are comments from the alignment input file:
# RDC data
Number of triangulated 3-point waters found: 0
Sum of charges from parm topology file = -41.00000000
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
56 4.2382E+03 5.2645E-05 0.0000E+00 H5T 1
BOND = 145.3984 ANGLE = 1915.0055 DIHED = 985.3029
VDWAALS = -215.4678 EEL = -140.9082 HBOND = 0.0000
1-4 VDW = 1004.5470 1-4 EEL = -1382.6198 RESTRAINT = 1926.9051
EAMBER = 2311.2581
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
Energy (this step): Align= 1926.905 CSA= 0.000
Alignment tensor: 17.553 43.682 18.576
43.682 -13.406 32.292
18.576 32.292 -4.147
===============================================================================
------------------------------------------------------------------------------
Final Restraint Analysis for coords: tensor-calc/amber_cycle1_align.x
Restraints, deviations, and energy contributions: pencut = 0.10
------------------------------------------------------------------------------
First atom Last atom curr. value target deviation penalty
------------------------------------------------------------------------------
| RMS deviation from ideal bonds : 0.0163
| RMS deviation from ideal angles: 6.942
------------------------------------------------------------------------------
Residual dipolar splittings:
------------------------------------------------------------------------------
First atom Last atom curr. value target deviation penalty distance
------------------------------------------------------------------------------
C8 RG5 1 -- H8 RG5 1: 0.000 13.020 -13.020 36.432 1.080
C8 RG 2 -- H8 RG 2: 0.000 12.350 -12.350 32.137 1.080
C1' RG 2 -- H1' RG 2: 0.000 -16.720 16.720 65.004 1.080
C8 RG 3 -- H8 RG 3: 0.000 20.050 -20.050 97.741 1.080
C2 RA 4 -- H2 RA 4: 0.000 30.520 -30.520 244.017 1.080
C8 RA 5 -- H8 RA 5: 0.000 18.140 -18.140 78.150 1.080
C2 RA 5 -- H2 RA 5: 0.000 18.020 -18.020 76.992 1.080
C8 RA 6 -- H8 RA 6: 0.000 22.140 -22.140 121.686 1.080
C2 RA 6 -- H2 RA 6: 0.000 20.040 -20.040 97.632 1.080
C6 RU 7 -- H6 RU 7: 0.000 14.110 -14.110 43.996 1.080
C1' RU 7 -- H1' RU 7: 0.000 -21.320 21.320 111.979 1.080
C8 RG 8 -- H8 RG 8: 0.000 20.220 -20.220 99.591 1.080
C2 RA 9 -- H2 RA 9: 0.000 27.480 -27.480 194.769 1.080
C8 RG 10 -- H8 RG 10: 0.000 24.840 -24.840 156.500 1.080
C1' RG 10 -- H1' RG 10: 0.000 -15.830 15.830 57.381 1.080
C8 RG 11 -- H8 RG 11: 0.000 22.630 -22.630 127.679 1.080
C6 RC 12 -- H6 RC 12: 0.000 18.960 -18.960 86.292 1.080
C8 RG 13 -- H8 RG 13: 0.000 16.560 -16.560 63.598 1.080
C1' RG 13 -- H1' RG 13: 0.000 12.640 -12.640 33.963 1.080
C1' RC 14 -- H1' RC 14: 0.000 -18.700 18.700 83.667 1.080
C8 RG 16 -- H8 RG 16: 0.000 18.210 -18.210 78.829 1.080
C6 RC 17 -- H6 RC 17: 0.000 10.700 -10.700 22.707 1.080
C1' RC 17 -- H1' RC 17: 0.000 -6.870 6.870 7.115 1.080
C8 RA 18 -- H8 RA 18: 0.000 12.700 -12.700 34.347 1.080
C2 RA 18 -- H2 RA 18: 0.000 17.240 -17.240 69.677 1.080
C6 RU 19 -- H6 RU 19: 0.000 -2.320 2.320 0.031 1.080
C1' RU 19 -- H1' RU 19: 0.000 -7.800 7.800 10.092 1.080
C8 RG 23 -- H8 RG 23: 0.000 21.250 -21.250 111.169 1.080
C8 RA 25 -- H8 RA 25: 0.000 29.430 -29.430 225.721 1.080
C2 RA 25 -- H2 RA 25: 0.000 17.900 -17.900 75.843 1.080
C8 RG 26 -- H8 RG 26: 0.000 32.850 -32.850 285.517 1.080
C1' RG 26 -- H1' RG 26: 0.000 -16.580 16.580 63.773 1.080
C6 RU 27 -- H6 RU 27: 0.000 19.540 -19.540 92.295 1.080
C6 RC 28 -- H6 RC 28: 0.000 8.500 -8.500 12.675 1.080
C8 RG 30 -- H8 RG 30: 0.000 18.130 -18.130 78.053 1.080
C1' RC 31 -- H1' RC 31: 0.000 -22.380 22.380 124.603 1.080
C1' RU 33 -- H1' RU 33: 0.000 -27.620 27.620 196.915 1.080
C6 RC 36 -- H6 RC 36: 0.000 26.900 -26.900 186.003 1.080
C1' RU 37 -- H1' RU 37: 0.000 -21.130 21.130 109.787 1.080
C1' RU 38 -- H1' RU 38: 0.000 -13.720 13.720 41.208 1.080
C1' RU 39 -- H1' RU 39: 0.000 -19.800 19.800 95.052 1.080
C6 RC 40 -- H6 RC 40: 0.000 12.600 -12.600 33.708 1.080
C1' RC 41 -- H1' RC 41: 0.000 -13.830 13.830 41.985 1.080
C6 RC3 42 -- H6 RC3 42: 0.000 21.230 -21.230 110.938 1.080
Total align constraint: 4017.25
Diagonalize the alignment matrix:
0.00000 1.00000 0.00000 0.00000
0.00000 0.00000 1.00000 0.00000
0.00000 0.00000 0.00000 1.00000
Diagonalize the moment of interia tensor:
960418.72968 0.62880 0.72424 0.28298 31.61271
3016169.37788 0.61944 -0.68656 0.38070 15.22399
3297190.89347 -0.47000 0.06409 0.88034 11.26231
------------------------------------------------------------------------------
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Received on Wed Sep 16 2009 - 09:30:02 PDT
