HI !!
I've modeled a cytosolic protein and trying to do MD
simulation studies on it using AMBER5. I'm facing two
problems:
1. I set up a water box of 216 TIP3 water molecules
(using solvateDontClip in Xleap)& then tried to
minimise first the solvent keeping the protein
constrained (protein has already been minimised in
vacuum ). This resulted in the bond, VanderWalls & EEL
energy becoming significantly large. I've tried using
Shake, but the Run stopped in between after about 800
cycles, displaying "LINMIN FAILURE". I dont have the
slightest idea about what it means or what am I
supposed to do about it.
2. Since the minimisation run, nevertheless, generated
a restart file, I proceeded with MD with constant
pressure and protein constrained to equilibriate the
solvent. Here, I've faced a lot of problem in
obtaining a stable pressure. Had to tighten TAUP to
0.01 (manual recommends 1-5ps). Also, even though I've
set TEMPO = 300, the temperature keeps hovering around
305K. How to stabilise these parameters?
Following are the input & output files:
#minimization
&cntrl
IMIN = 1,
NTX = 1, IREST = 0,
NTXO = 1, NTPR = 100,
NTF = 1, NTB = 1, IDIEL = 1, DIELC = 1,
CUT = 8.0, NSNB = 25, SCNB = 2.0, SCEE=1.2,
NTR = 1, IBELLY = 0,
MAXCYC = 2000, NCYC = 200, NTMIN = 1,
DX0 = 0.01, DXM = 0.05, DRMS = 0.0001,
NRUN = 0, INIT = 3,
TEMP0=20, TEMPI= 0,
&end
Group 1
1.000
RES 1 156
END
END
-------------------------------------------------------------------------------
FINAL RESULTS
NSTEP ENERGY RMS GMAX
NAME NUMBER
2000 -8.3194E+04 5.0185E-01 3.8746E+01
SG 305
BOND = 6569.9868 ANGLE = 404.5978
DIHED = 840.2151
VDWAALS = 16377.9255 EEL = -116880.0034
HBOND = 0.0000
1-4 VDW = 505.5352 1-4 EEL = 8916.7494
CONSTRAINT = 70.7141
EAMBER = -83264.9935
# If NTF = 3 ; NTC = 3 is used I get :
FINAL RESULTS
NSTEP ENERGY RMS GMAX
NAME NUMBER
749 -6.0820E+04 1.4074E+01 4.5064E+01
O 12545
BOND = 0.0000 ANGLE = 436.7083
DIHED = 868.4042
VDWAALS = 3834.1585 EEL = -75732.8212
HBOND = 0.0000
1-4 VDW = 605.7295 1-4 EEL = 9163.0613
CONSTRAINT = 4.8569
EAMBER = -60824.7595
***** REPEATED LINMIN FAILURE *****
Next I had put the restart file from the above run in
to MD with the following input file.
#MD
&cntrl
IMIN = 0,
NTX = 7, IREST = 1, NTRX = 1,
NTXO = 1, NTPR = 100, NTWXM = 0,
NTF = 2, NTB = 2, IDIEL = 1, DIELC = 1,
CUT = 8.0, NSNB = 25, SCNB = 2.0, SCEE = 1.2,
NTR = 1, IBELLY = 0,
NRUN = 1, NSTLIM = 1000,
NDFMIN = 6, NTCM = 1, NSCM = 100, INIT = 4, DT =
0.002,
TEMP0=300, TEMPI=300, NTT = 5, TAUTP = 2.0, TAUTS =
0.1, VLIMIT = 20.0,
NTP = 1, NPSCAL = 1, PRES0 = 1.0, COMP =44.6,
TAUP = 0.01,
NTC = 2, TOL = 0.0005,
IMGSLT = 1,
&end
Group 1
1.000
RES 1 156
END
END
#output at 100ps of solvent equilibriation
NSTEP = 500 TIME(PS) = 100.000 TEMP(K) =
306.06 PRESS = -13.56
Etot = -50496.5096 EKtot = 13891.6135 EPtot
= -64388.1231
BOND = 457.5937 ANGLE = 1289.0477 DIHED
= 1044.3666
1-4 NB = 579.0341 1-4 EEL = 8903.8669
VDWAALS = 8439.7900
EELEC = -85333.4539 EHBOND = 0.0000
CONSTRAINT = 231.6318
EAMBER (non-constraint) = -64619.7549
EKCMT = 5949.0999 VIRIAL = 6014.6332 VOLUME
= 223779.1841
T_SOLUTE = 312.0014 T_SOLVENT = 305.1337
Density = 1.0106
------------------------------------------------------------------------------
RESULT OF LEAST SQUARE FIT OVER 100 STEPS
ENERGY DRIFT PER STEP = 0.482713
ETOT(AT X=0) = -5.050E+04
NB-update: NPAIRS = 2947114 HBPAIR = 881596
NB-update: NPAIRS = 2950392 HBPAIR = 883136
NB-update: NPAIRS = 2952518 HBPAIR = 882360
NB-update: NPAIRS = 2948627 HBPAIR = 881576
NSTEP = 600 TIME(PS) = 100.200 TEMP(K) =
300.44 PRESS = 18.89
Etot = -50483.7521 EKtot = 13636.3004 EPtot
= -64120.0525
BOND = 476.0253 ANGLE = 1341.7558 DIHED
= 1058.1273
1-4 NB = 582.5088 1-4 EEL = 8896.3333
VDWAALS = 8394.1504
EELEC = -85103.2590 EHBOND = 0.0000
CONSTRAINT = 234.3054
EAMBER (non-constraint) = -64354.3579
EKCMT = 5797.7807 VIRIAL = 5706.4556 VOLUME
= 223882.0072
T_SOLUTE = 305.0666 T_SOLVENT = 299.7129
Density = 1.0101
------------------------------------------------------------------------------
A V E R A G E S O V E R 1000 S T E P S
NSTEP = 1000 TIME(PS) = 101.000 TEMP(K) =
305.10 PRESS = 1.73
Etot = -50477.5774 EKtot = 13847.8916 EPtot
= -64325.4690
BOND = 449.7897 ANGLE = 1303.5053 DIHED
= 1053.4361
1-4 NB = 580.0433 1-4 EEL = 8906.4369
VDWAALS = 8370.4212
EELEC = -85220.0855 EHBOND = 0.0000
CONSTRAINT = 230.9839
EAMBER (non-constraint) = -64556.4529
EKCMT = 5923.5515 VIRIAL = 5915.2117 VOLUME
= 223540.3806
T_SOLUTE = 309.2204 T_SOLVENT = 304.4540
Density = 1.0116
------------------------------------------------------------------------
Although on average it remains near the set point, it
fluctuates in the intermediate steps.
If I increase the value of TAUP to 0.5, it fluctuates
even more.
PLEASE HELP me sort these out.
Thank you
Suvendu
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Received on Thu Jul 25 2002 - 00:49:28 PDT
