AMBER Archive (2005)

Subject: AMBER: Dipolar coupling refinement

From: s0344557_at_sms.ed.ac.uk
Date: Fri Oct 21 2005 - 08:04:39 CDT

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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