AMBER Archive (2008)

Subject: AMBER: NMR refinement

From: Wenyong Tong (wenyong_tong_at_yahoo.com)
Date: Thu Jan 17 2008 - 20:54:04 CST

Hello,

Here is my result of annealing with NMR refinement. Could you please give me some suggestions about this ?

The structure is a glycolipd with five sugars. I input all the distance restrains this time. I did double check my assignments of NOESY.

&cntrl
  ntwx=500, ntpr=500, ntwe=500, ntwv=500,
  ntt=1, temp0=1000.0, tempi=5.0,
  igb=1, saltcon=0.05, offset=0.13,
  scnb=2.0, scee=1.2, dielc=80, cut=100.0,
  ntb=0, ntc=2, ntf=2,
  nstlim=100000, dt=0.0020,
  vlimit=10, rgbmax=30.0,
  ntp=0,
  ibelly=0, ntr=0,
  imin=0, irest=0, ntx=1, nmropt=1,
  /
 &wt type='TEMP0', istep1=1, istep2=5000, value1=5.0, value2=1000.0,
  /
 &wt type='TEMP0', istep1=5001, istep2=10000, value1=1000, value2=1000.0,
  /
 &wt type='TEMP0', istep1=10001, istep2=100000, value1=1000.0, value2=5.0,
 /
 &wt type='TAUTP', istep1=0, istep2=10000,value1=0.2, value2=0.2,
  /
 &wt type='TAUTP', istep1=10001,istep2=18000,value1=4.0, value2=2.0,
  /
 &wt type='TAUTP', istep1=18001,istep2=88000,value1=1.0, value2=1.0,
  /
 &wt type='TAUTP', istep1=88001,istep2=98000,value1=0.5, value2=0.5,
  /
 &wt type='TAUTP', istep1=98001,istep2=100000,value1=0.01, value2=0.05,
  /
 &wt type='REST', istep1=0,istep2=10000,value1=0.1, value2=1.0,
 /
 &wt type='REST', istep1=10001,istep2=100000,value1=1.0, value2=1.0,
 /
 &wt
  type='END'/
LISTOUT=POUT
DISANG=RST.dist

KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000

   Translational and rotational motion removed

   KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000

 NSTEP = 100000 TIME(PS) = 400.000 TEMP(K) = 5.83 PRESS = 0.0
 Etot = 113.8921 EKtot = 2.5555 EPtot = 111.3366
 BOND = 16.6879 ANGLE = 67.8741 DIHED = -21.9361
 1-4 NB = 45.8247 1-4 EEL = 1142.0964 VDWAALS = -32.7528
 EELEC = -762.9891 EGB = -540.2703 RESTRAINT = 196.8019
 EAMBER (non-restraint) = -85.4652
 ------------------------------------------------------------------------------

 NMR restraints: Bond = 196.802 Angle = 0.000 Torsion = 0.000
===============================================================================

      A V E R A G E S O V E R 100000 S T E P S

 NSTEP = 100000 TIME(PS) = 400.000 TEMP(K) = 534.38 PRESS = 0.0
 Etot = 487.3202 EKtot = 234.1512 EPtot = 253.1690
 BOND = 50.0900 ANGLE = 142.9896 DIHED = -6.9437
 1-4 NB = 51.7259 1-4 EEL = 1136.9617 VDWAALS = -26.4569
 EELEC = -738.2782 EGB = -555.6497 RESTRAINT = 198.7303
 EAMBER (non-restraint) = 54.4387
 ------------------------------------------------------------------------------

 NMR restraints: Bond = 196.802 Angle = 0.000 Torsion = 0.000
===============================================================================

      R M S F L U C T U A T I O N S

 NSTEP = 100000 TIME(PS) = 400.000 TEMP(K) = 302.00 PRESS = 0.0
 Etot = 206.9585 EKtot = 132.3282 EPtot = 81.9477
 BOND = 17.2825 ANGLE = 37.8038 DIHED = 9.1470
 1-4 NB = 5.2395 1-4 EEL = 12.7741 VDWAALS = 5.7178
 EELEC = 18.2675 EGB = 11.5462 RESTRAINT = 22.5727
 EAMBER (non-restraint) = 59.3750
 ------------------------------------------------------------------------------

Thanks in advance !

Wenyong

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