AMBER Archive (2007)

Subject: AMBER: Request reg parameter for vitamin e

From: Rama krishnan (ramki_rpcr_at_yahoo.com)
Date: Tue Nov 06 2007 - 01:11:47 CST

Sir,
   
     i tried to simulate protein complex with vitamin e using AMBER GB model. In my trajectory the ligand getting unusual conformation. So please guide me for correct result
   
  herewith i have attached the result files for check
   
  input ligand -----> input-vit.pdb
  prepin file ------> vit.prepin
  frcmod file -------> vit.frcmod
  control files
      energy minimization --> min.in
      equilibration ---> tmp.in
      produciton run ----> md.in
   
  xleap log file -------------> leap.log
   
  Thank you very much
   
  With regards
   
   

   C.Ramakrishnan.
       Lecturer - Bioinformatics
       SRM Arts & Science College
       Kattankulathur - 603203
         Contact :
         Mobile - 98405 95180
       College - 91 44 27454863
       Alt.email: ramki.rpcr_at_gmail.com

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Molecular Dynamics for 1 ns with 2 fs time-step
&cntrl
  imin=0
  ntc=2, ntf=2,
  cut=12.0, igb=2, saltcon=0.2, gbsa=1,
  intdiel=1.0, extdiel=78.5,
  ntpr=50, ntwx=100,
  nstlim=1000000, dt=0.001,
  ntt=1, tempi=300.0, temp0=300.0, tautp=1.0,
  ntx=5, irest=0, ntb=0,
  nscm=1000,
/

minimization

&cntrl
  imin=1, maxcyc=500,
  cut=300.0, igb=2, saltcon=0.2, gbsa=1,
  intdiel=1.0, extdiel=78.5,
  ntpr=10, ntx=1, ntb=0,
  ntr=1
/
  keep all atoms restrained
  5.0
RES 1 122
END
END

equilibration

&cntrl
  imin=0
  ntc=2, ntf=2,
  cut=12.0, igb=2, saltcon=0.2, gbsa=1,
  intdiel=1.0, extdiel=78.5,
  ntpr=50,
  nstlim=10000, dt=0.002,
  ntt=1, tempi=0.0, temp0=300.0, tautp=1.0,
  ntx=1, irest=0, ntb=0,
  nscm=1000,
  ntr=1
/
  keep all atoms restrained
  5.0
RES 1 122
END
END

remark goes here
MASS

BOND
cg-c2 625.00 1.307 same as c1-c2

ANGLE
cg-c1-c3 56.400 177.990 same as c1-c1-c3
cg-c2-c2 70.300 121.620 same as c1-c2-c2
c1-cg-c2 60.800 180.000 same as c1-c1-c2
c1-c2-c 67.966 117.825 Calculated with empirical approach
cg-cg-c2 60.800 180.000 same as c1-cg-c2
cg-c2-c1 72.300 116.770 same as c1-c2-c1

DIHE
c1-cg-c2-c2 1 0.000 180.000 2.000 same as X -c1-c2-X
cg-cg-c2-c1 1 0.000 180.000 2.000 same as X -c1-c2-X

IMPROPER

NONBON


    0 0 2

This is a remark line
molecule.res
VIT INT 0
CORRECT OMIT DU BEG
  0.0000
   1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
   2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
   3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
   4 C10 cg M 3 2 1 1.540 111.208 180.000 -0.03698
   5 C11 c1 E 4 3 2 1.581 86.374 105.437 -0.09135
   6 C3 c2 M 4 3 2 1.571 156.464 -78.224 -0.07051
   7 C2 c2 M 6 4 3 1.431 122.890 -28.335 -0.37631
   8 C8 c1 E 7 6 4 1.520 119.046 -0.739 0.32624
   9 C7 c M 7 6 4 1.434 119.695 179.985 0.61333
  10 O2 o E 9 7 6 1.467 114.600 -177.639 -0.53039
  11 C6 c2 M 9 7 6 1.441 120.444 -0.032 -0.39360
  12 C13 c1 E 11 9 7 1.550 123.007 179.269 0.32699
  13 C5 c2 M 11 9 7 1.450 119.647 0.069 -0.40100
  14 C12 c1 E 13 11 9 1.520 121.577 175.610 0.31087
  15 C4 c2 M 13 11 9 1.447 119.075 -0.089 0.33626
  16 O1 os M 15 13 11 1.429 121.942 -179.988 -0.36504
  17 C9 c3 M 16 15 13 1.517 123.871 -137.657 -0.16752
  18 C14 c1 E 17 16 15 1.659 135.819 73.248 0.33901
  19 C15 c1 M 17 16 15 1.478 92.875 -148.364 0.01804
  20 C16 cg M 19 17 16 1.578 131.803 147.717 -0.09094
  21 C17 cg M 20 19 17 1.557 113.335 154.445 -0.03567
  22 C18 c2 M 21 20 19 1.634 118.129 166.462 -0.08544
  23 C19 c1 E 22 21 20 1.549 94.910 105.095 0.15858
  24 C20 c1 M 22 21 20 1.627 140.143 -139.190 -0.04390
  25 C21 c1 M 24 22 21 1.586 127.064 154.741 -0.06222
  26 C22 c1 M 25 24 22 1.588 117.469 -176.105 -0.18543
  27 C23 c2 M 26 25 24 1.626 117.871 -177.799 -0.02929
  28 C1 c1 E 27 26 25 1.495 99.716 60.351 0.35188
  29 C24 c1 M 27 26 25 1.558 115.858 178.171 -0.04125
  30 C25 c1 M 29 27 26 1.629 112.801 176.882 0.03335
  31 C26 c1 M 30 29 27 1.609 117.572 -178.293 -0.11561
  32 C27 c2 M 31 30 29 1.544 132.141 -115.920 -0.45571
  33 C29 c1 E 32 31 30 1.541 109.318 -147.101 0.38158
  34 C28 c1 M 32 31 30 1.555 110.681 92.381 0.38203

LOOP
   C9 C11
   C4 C3

IMPROPER
   C4 C2 C3 C10
   C8 C3 C2 C7
   C6 C2 C7 O2
  C13 C5 C6 C7
  C12 C6 C5 C4
   C5 C3 C4 O1
  C19 C20 C18 C17
  C22 C1 C23 C24
  C26 C29 C27 C28

DONE
STOP

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