Dear Amber users,
I am trying to use the residue dipolar coupling(RDC) constants to refine my
tetrasaccharide. I prepared the RST-AC.f manully with 10 RDCs of two rings and
the alignment saupe parameters are from one of the best fitting results of the
RDCs to the structure. But when running the refinement with this restraint, I
did not improve the structure at all. There must be something I missed out.
Could anybody give some comments on this? Such as how do you choose the
s11,s12...parms and what other things need to be noticed. Many thanks.
INPUT:
&cntrl
imin = 0, ntpr = 200, ntwx = 200, ntwe = 200, ntwr = 20000,
nstlim = 200000, dt = 0.002, irest = 1, ntx = 5,
ntb = 2, pres0 = 1.0, ntp = 1, taup = 2.0,
cut = 8, ntr = 0, ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0, ntt = 1,
iscale = 5, nmropt = 1,
&end
&wt type = 'END', &end
LISTOUT = POUT
DIPOLE = RST-AC.f
RST-AC.f
&align
ndip = 10, dcut = -1.0, gigj = 10*7.847, dwt = 10*0.1,
s11 = 1.635, s22 = 13.637, s12 = -1.0059, s13 = 0.64902, s23 = -0.45367,
id(1) = 12, jd(1) = 13, dobs(1) = -3.4,
id(2) = 14, jd(2) = 15, dobs(2) = 5.8,
id(3) = 16, jd(3) = 17, dobs(3) = 6.1,
id(4) = 28, jd(4) = 29, dobs(4) = 5.4,
id(5) = 9, jd(5) = 10, dobs(5) = 6.2,
id(6) = 53, jd(6) = 54, dobs(6) = 5.1,
id(7) = 66, jd(7) = 67, dobs(7) = -3.1,
id(8) = 74, jd(8) = 75, dobs(8) = -3.0,
id(9) = 78, jd(9) = 79, dobs(9) = -4.8,
id(10) = 56, jd(10) = 57, dobs(10) = -3.6,
&end
OUTPUT: only the rear part
A V E R A G E S O V E R 200000 S T E P S
NSTEP = 200000 TIME(PS) = 1120.000 TEMP(K) = 299.94 PRESS = 0.8
Etot = -20168.4858 EKtot = 4419.2561 EPtot = -24587.7419
BOND = 27.5717 ANGLE = 60.3247 DIHED = 30.3226
1-4 NB = 26.9627 1-4 EEL = 290.3671 VDWAALS = 3446.0113
EELEC = -28471.4132 EHBOND = 0.0000 RESTRAINT = 2.1112
EAMBER (non-restraint) = -24589.8531
EKCMT = 2183.2718 VIRIAL = 2181.9753 VOLUME = 74394.8100
Density = 1.0035
Ewald error estimate: 0.1152E-03
------------------------------------------------------------------------------
===============================================================================
NMR restraints for step 200000
Energy (this step): Bond = 0.000 Angle = 0.000 Torsion = 0.000
Energy (tot. run) : Bond = 0.000 Angle = 0.000 Torsion = 0.000
DEVIATIONS: Target=(r2+r3)/2 Target = closer of r2/r3
This step Entire run This step Entire run
ave. rms ave. rms ave. rms ave. rms
Bond 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
Angle 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
Torsion 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
Energy (this step): Align= 1.644
Alignment tensor: -4.609 9.473 15.706
9.473 -15.996 -15.870
15.706 -15.870 20.605
===============================================================================
R M S F L U C T U A T I O N S
NSTEP = 200000 TIME(PS) = 1120.000 TEMP(K) = 2.74 PRESS = 216.4
Etot = 15.2477 EKtot = 40.3926 EPtot = 43.2251
BOND = 4.4363 ANGLE = 6.2107 DIHED = 2.7522
1-4 NB = 2.2824 1-4 EEL = 7.0188 VDWAALS = 68.7542
EELEC = 86.6415 EHBOND = 0.0000 RESTRAINT = 1.6803
EAMBER (non-restraint) = 41.5448
EKCMT = 31.9473 VIRIAL = 348.5850 VOLUME = 143.0519
Density = 0.0019
Ewald error estimate: 0.8619E-04
------------------------------------------------------------------------------
NMR restraints on final step:
------------------------------------------------------------------------------
Final Restraint Analysis for coords: restrt
Restraints, deviations, and energy contributions: pencut = 0.10
------------------------------------------------------------------------------
First atom Last atom curr. value target deviation penalty
------------------------------------------------------------------------------
| RMS deviation from ideal bonds : 0.0036
| RMS deviation from ideal angles: 4.046
------------------------------------------------------------------------------
Residual dipolar splittings:
------------------------------------------------------------------------------
First atom Last atom curr. value target deviation penalty distance
------------------------------------------------------------------------------
C2 TAP 1 -- H6 TAP 1: -1.952 -3.400 1.448 0.210 1.090
C1 TAP 1 -- H7 TAP 1: 6.432 5.800 0.632 0.040 1.090
C5 TAP 1 -- H9 TAP 1: 7.247 6.100 1.147 0.131 1.090
C6 TAP 1 -- H10 TAP 1: 7.492 5.400 2.092 0.438 1.090
C3 TAP 1 -- H4 TAP 1: 6.946 6.200 0.746 0.056 1.090
C13 TAP 1 -- H17 TAP 1: 4.388 5.100 -0.712 0.051 1.090
C14 TAP 1 -- H18 TAP 1: -1.570 -3.100 1.530 0.234 1.090
C15 TAP 1 -- H19 TAP 1: -3.248 -3.000 -0.248 0.006 1.090
C18 TAP 1 -- H25 TAP 1: -2.836 -4.800 1.964 0.386 1.090
C16 TAP 1 -- H24 TAP 1: -2.634 -3.600 0.966 0.093 1.090
Total align constraint: 1.64
# Pearson r rms error
-----------------------------------
Align correlation: 10 0.98325 2.38706 1.28233
Diagonalize the alignment matrix:
-30.61594 -0.51513 0.76128 0.39383
-0.05778 0.78669 0.60233 -0.13532
30.67372 0.34023 -0.24011 0.90917
Diagonalize the moment of interia tensor:
113820935.29519 0.45436 0.89040 0.02729 83.07800
118324329.63457 -0.47544 0.26829 -0.83784 80.00677
119609170.40057 -0.75334 0.36770 0.54523 79.10867
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Received on Fri Oct 21 2005 - 14:53:01 PDT
