AMBER Archive (2009)

Subject: Re: [AMBER] Error in binding energy (MM PBSA)

From: Vikas Sharma (vs_vikassharma_at_yahoo.co.in)
Date: Fri May 08 2009 - 01:50:40 CDT

Dear Dr. Ray Luo

Thanks for the reply..
Actually i used antechamber (bcc charges for the ligand)...could this be the reason?
Shall i use rersp charges n also do Gaussian calculations?

i checked the ligand inpcrd and prmtop files but couldnot understand...i am pasting both the files below...if you could figure out the problem....
i am waiting for your suggestion

Thanks a lot

 1. ligand.inpcrd

LIG
    42
   3.5369136 1.4228577 -0.0000019 2.9898844 1.5587730 -0.9446109
   3.4532155 2.3345782 0.6079136 3.1094366 0.5728906 0.5521026
   5.0218010 1.1425952 -0.3020668 5.8284397 2.4472630 -0.1650409
   6.6607395 2.2928284 0.5389677 5.1730969 3.2458307 0.2128684
   6.2289866 2.7350844 -1.1482606 5.1587712 0.6298757 -1.7039794
   5.9629998 -0.4189192 -1.9840626 6.1439254 -0.8707535 -3.1895134
   7.0902138 -0.8819709 -3.5986264 5.3428892 -1.2161498 -3.7353003
   6.6353788 -1.0548006 -0.9998054 6.4378385 -0.7651789 0.3411246
   7.0742278 -1.3722019 1.2984812 7.3971213 -0.8417493 2.1202231
   7.2552107 -2.3842164 1.2354589 5.5442672 0.1808809 0.7040325
   5.3957378 0.4476671 2.0703283 4.9690135 -0.7391412 2.7443405
   5.6164421 -1.5726809 2.4344249 3.9273430 -0.9611484 2.4693216
   5.0856452 -0.5358840 4.2664060 6.1498631 -0.4938290 4.5454628
   4.6044618 -1.3774604 4.7862249 4.3969786 0.7830848 4.6634696
   4.8724402 1.6221255 4.1343694 4.4916678 0.9332366 5.7490517
   3.0113230 0.7214321 4.3155364 2.3609953 1.8714296 4.7476008
   1.8229404 1.9384206 6.0924090 2.0274721 0.5861365 7.1841940
   1.1075728 3.1361897 6.5394253 0.7023348 3.1824600 7.5437645
   0.9394004 4.2707969 5.6264409 0.0666123 5.6942303 6.1504429
   1.5064754 4.2028703 4.2925695 1.3408832 5.5603709 3.2006578
   2.2005458 3.0125773 3.8707284 2.6085594 2.9853354 2.8668167

2. ligand.prmtop

%VERSION VERSION_STAMP = V0001.000 DATE = 04/14/09 15:30:52
%FLAG TITLE
%FORMAT(20a4)
LIG
%FLAG POINTERS
%FORMAT(10I8)
      42 9 18 25 37 36 56 49 0 0
     208 1 25 36 49 17 29 13 13 0
       0 0 0 0 0 0 0 0 42 0
       0
%FLAG ATOM_NAME
%FORMAT(20a4)
CM1 H9 H10 H11 C1 CM2 H12 H13 H14 N2 C3 NH1 H15 H16 N4 C5 NH2 H17 H18 N6
O7 C8 H1 H2 C9 H3 H4 C10 H5 H6 O11 C12 C13 Cl1 C14 H7 C15 Cl2 C16 Cl3
C17 H8
%FLAG CHARGE
%FORMAT(5E16.8)
  7.50376092E+01 1.75061636E+01 1.75061636E+01 1.75061636E+01 7.80533998E+01
  7.50376092E+01 1.75061636E+01 1.75061636E+01 1.75061636E+01 8.35875123E+01
  8.49013402E+01 8.08742119E+01 2.19542270E+01 2.19542270E+01 8.18727939E+01
  8.36786238E+01 8.08742119E+01 2.19542270E+01 2.19542270E+01 8.45132052E+01
  1.08967532E+02 7.56298339E+01 1.75061636E+01 1.75061636E+01 7.43214728E+01
  1.75061636E+01 1.75061636E+01 7.56298339E+01 1.75061636E+01 1.75061636E+01
  1.07203613E+02 7.37110257E+01 7.43178283E+01 1.26127472E+02 7.28892000E+01
  1.82223000E+01 7.43178283E+01 1.26127472E+02 7.43178283E+01 1.26127472E+02
  7.28892000E+01 1.82223000E+01
%FLAG MASS
%FORMAT(5E16.8)
  1.20100000E+01 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.20100000E+01
  1.20100000E+01 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.40100000E+01
  1.20100000E+01 1.40100000E+01 1.00800000E+00 1.00800000E+00 1.40100000E+01
  1.20100000E+01 1.40100000E+01 1.00800000E+00 1.00800000E+00 1.40100000E+01
  1.60000000E+01 1.20100000E+01 1.00800000E+00 1.00800000E+00 1.20100000E+01
  1.00800000E+00 1.00800000E+00 1.20100000E+01 1.00800000E+00 1.00800000E+00
  1.60000000E+01 1.20100000E+01 1.20100000E+01 3.54500000E+01 1.20100000E+01
  1.00800000E+00 1.20100000E+01 3.54500000E+01 1.20100000E+01 3.54500000E+01
  1.20100000E+01 1.00800000E+00
%FLAG ATOM_TYPE_INDEX
%FORMAT(10I8)
       1 2 2 2 1 1 2 2 2 3
       4 3 5 5 3 4 3 5 5 3
       6 1 7 7 1 2 2 1 7 7
       6 4 4 8 4 9 4 8 4 8
       4 9
%FLAG NUMBER_EXCLUDED_ATOMS
%FORMAT(10I8)
      13 6 5 4 13 8 4 3 2 8
       7 4 2 1 6 6 4 2 1 5
       7 9 5 4 7 5 4 6 3 2
       7 9 8 4 6 3 5 3 3 2
       1 1
%FLAG NONBONDED_PARM_INDEX
%FORMAT(10I8)
       1 2 4 7 11 16 22 29 37 2
       3 5 8 12 17 23 30 38 4 5
       6 9 13 18 24 31 39 7 8 9
      10 14 19 25 32 40 11 12 13 14
      15 20 26 33 41 16 17 18 19 20
      21 27 34 42 22 23 24 25 26 27
      28 35 43 29 30 31 32 33 34 35
      36 44 37 38 39 40 41 42 43 44
      45
%FLAG RESIDUE_LABEL
%FORMAT(20a4)
WRA
%FLAG RESIDUE_POINTER
%FORMAT(10I8)
       1
%FLAG BOND_FORCE_CONSTANT
%FORMAT(5E16.8)
  3.37300000E+02 3.03100000E+02 3.13800000E+02 3.32700000E+02 5.99800000E+02
  4.84700000E+02 3.81800000E+02 4.01200000E+02 5.97700000E+02 4.62600000E+02
  3.58500000E+02 3.01500000E+02 3.35900000E+02 3.72400000E+02 4.78400000E+02
  3.22800000E+02 3.44300000E+02
%FLAG BOND_EQUIL_VALUE
%FORMAT(5E16.8)
  1.09200000E+00 1.53500000E+00 1.47700000E+00 1.45800000E+00 1.27900000E+00
  1.34100000E+00 1.41400000E+00 1.01400000E+00 1.28000000E+00 1.35500000E+00
  1.44100000E+00 1.43900000E+00 1.09300000E+00 1.37300000E+00 1.38700000E+00
  1.72900000E+00 1.08700000E+00
%FLAG ANGLE_FORCE_CONSTANT
%FORMAT(5E16.8)
  6.32000000E+01 6.64000000E+01 6.66000000E+01 3.94000000E+01 4.64000000E+01
  6.61000000E+01 6.32000000E+01 6.71500000E+01 7.05880000E+01 7.26000000E+01
  7.80000000E+01 5.01000000E+01 6.73000000E+01 7.33000000E+01 4.01000000E+01
  7.33000000E+01 4.90000000E+01 6.71090000E+01 7.29000000E+01 6.54000000E+01
  5.08000000E+01 6.78000000E+01 3.92000000E+01 4.64000000E+01 6.24000000E+01
  6.98000000E+01 5.84000000E+01 6.72000000E+01 4.85000000E+01
%FLAG ANGLE_EQUIL_VALUE
%FORMAT(5E16.8)
  1.93085858E+00 1.90520223E+00 1.91602327E+00 1.89106506E+00 1.92073567E+00
  2.01236549E+00 2.15914774E+00 1.91820494E+00 1.86375064E+00 2.16892159E+00
  1.98653461E+00 2.00241711E+00 2.06245646E+00 2.14186898E+00 1.99718112E+00
  2.14186898E+00 2.05844220E+00 2.00678043E+00 2.05076275E+00 1.87204096E+00
  1.89926811E+00 1.89228679E+00 1.91200902E+00 1.92108473E+00 2.05250808E+00
  2.08043336E+00 2.09265067E+00 2.09387240E+00 2.09457053E+00
%FLAG DIHEDRAL_FORCE_CONSTANT
%FORMAT(5E16.8)
  1.60000000E-01 0.00000000E+00 0.00000000E+00 1.55555556E-01 4.15000000E+00
  6.75000000E-01 1.50000000E+00 8.00000000E-01 3.83333333E-01 2.50000000E-01
  9.00000000E-01 3.62500000E+00 1.10000000E+00
%FLAG DIHEDRAL_PERIODICITY
%FORMAT(5E16.8)
  3.00000000E+00 3.00000000E+00 2.00000000E+00 3.00000000E+00 2.00000000E+00
  2.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00 1.00000000E+00
  2.00000000E+00 2.00000000E+00 2.00000000E+00
%FLAG DIHEDRAL_PHASE
%FORMAT(5E16.8)
  0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 3.14159400E+00
  3.14159400E+00 0.00000000E+00 3.14159400E+00 0.00000000E+00 0.00000000E+00
  3.14159400E+00 3.14159400E+00 3.14159400E+00
%FLAG SOLTY
%FORMAT(5E16.8)
  0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
  0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
  0.00000000E+00 0.00000000E+00 0.00000000E+00
%FLAG LENNARD_JONES_ACOEF
%FORMAT(5E16.8)
  1.04308023E+06 9.71708117E+04 7.51607703E+03 9.95480466E+05 8.96776989E+04
  9.44293233E+05 9.24822270E+05 8.61541883E+04 8.82619071E+05 8.19971662E+05
  2.56678134E+03 1.07193646E+02 2.12601181E+03 2.27577561E+03 1.39982777E-01
  6.28541240E+05 5.33379252E+04 5.89818288E+05 5.57281136E+05 1.03954408E+03
  3.61397723E+05 6.78771368E+04 4.98586848E+03 6.20665997E+04 6.01816484E+04
  5.94667300E+01 3.63097246E+04 3.25969625E+03 1.83982239E+06 1.74057868E+05
  1.76079018E+06 1.63123475E+06 4.83020816E+03 1.11729277E+06 1.22102013E+05
  3.24095688E+06 8.59947003E+04 6.55825601E+03 7.91627154E+04 7.62451550E+04
  8.90987508E+01 4.68711055E+04 4.33325458E+03 1.54217681E+05 5.71629601E+03
%FLAG LENNARD_JONES_BCOEF
%FORMAT(5E16.8)
  6.75612247E+02 1.26919150E+02 2.17257828E+01 7.36907417E+02 1.36131731E+02
  8.01323529E+02 5.99015525E+02 1.12529845E+02 6.53361429E+02 5.31102864E+02
  2.06278363E+01 2.59456373E+00 2.09604198E+01 1.82891803E+01 9.37598976E-02
  5.85549272E+02 1.04986921E+02 6.33305958E+02 5.19163331E+02 1.46567808E+01
  4.95732238E+02 1.06076943E+02 1.76949863E+01 1.13252061E+02 9.40505980E+01
  1.93248820E+00 8.66220817E+01 1.43076527E+01 1.11939599E+03 2.11915736E+02
  1.22266505E+03 9.92485818E+02 3.53019992E+01 9.73951183E+02 1.77491593E+02
  1.85348706E+03 1.18043746E+02 2.00642027E+01 1.26451907E+02 1.04660679E+02
  2.33864085E+00 9.73010751E+01 1.63092814E+01 1.97211104E+02 1.85196588E+01
%FLAG BONDS_INC_HYDROGEN
%FORMAT(10I8)
       0 3 1 0 6 1 0 9 1 15
      18 1 15 21 1 15 24 1 33 36
       8 33 39 8 48 51 8 48 54 8
      63 66 13 63 69 13 72 75 1 72
      78 1 81 84 13 81 87 13 102 105
      17 120 123 17
%FLAG BONDS_WITHOUT_HYDROGEN
%FORMAT(10I8)
       0 12 2 12 15 2 12 27 3 12
      57 4 27 30 5 30 33 6 30 42
       7 42 45 9 45 48 10 45 57 10
      57 60 11 60 63 12 63 72 2 72
      81 2 81 90 12 90 93 14 93 96
      15 93 120 15 96 99 16 96 102 15
     102 108 15 108 111 16 108 114 15 114
     117 16 114 120 15
%FLAG ANGLES_INC_HYDROGEN
%FORMAT(10I8)
       3 0 6 4 3 0 9 4 3 0
      12 5 6 0 9 4 6 0 12 5
       9 0 12 5 12 15 18 5 12 15
      21 5 12 15 24 5 18 15 21 4
      18 15 24 4 21 15 24 4 30 33
      36 12 30 33 39 12 36 33 39 15
      45 48 51 17 45 48 54 17 51 48
      54 15 60 63 66 21 60 63 69 21
      63 72 75 5 63 72 78 5 66 63
      69 23 66 63 72 24 69 63 72 24
      72 81 84 24 72 81 87 24 75 72
      78 4 75 72 81 5 78 72 81 5
      84 81 87 23 84 81 90 21 87 81
      90 21 93 120 123 29 96 102 105 29
     105 102 108 29 114 120 123 29
%FLAG ANGLES_WITHOUT_HYDROGEN
%FORMAT(10I8)
       0 12 15 1 0 12 27 2 0 12
      57 3 12 27 30 6 12 57 45 7
      12 57 60 8 15 12 27 2 15 12
      57 3 27 12 57 9 27 30 33 10
      27 30 42 11 30 42 45 13 33 30
      42 14 42 45 48 16 42 45 57 16
      45 57 60 18 48 45 57 19 57 60
      63 20 60 63 72 22 63 72 81 1
      72 81 90 22 81 90 93 25 90 93
      96 26 90 93 120 26 93 96 99 27
      93 96 102 28 93 120 114 28 96 93
     120 28 96 102 108 28 99 96 102 27
     102 108 111 27 102 108 114 28 108 114
     117 27 108 114 120 28 111 108 114 27
     117 114 120 27
%FLAG DIHEDRALS_INC_HYDROGEN
%FORMAT(10I8)
       0 12 15 18 1 0 12 15 21 1
       0 12 15 24 1 3 0 12 15 1
       3 0 12 27 4 3 0 12 57 4
       6 0 12 15 1 6 0 12 27 4
       6 0 12 57 4 9 0 12 15 1
       9 0 12 27 4 9 0 12 57 4
      18 15 12 27 4 18 15 12 57 4
      21 15 12 27 4 21 15 12 57 4
      24 15 12 27 4 24 15 12 57 4
      27 30 33 36 6 27 30 33 39 6
      36 33 30 42 6 39 33 30 42 6
      42 45 48 51 6 42 45 48 54 6
      51 48 45 57 6 54 48 45 57 6
      57 60 63 66 9 57 60 63 69 9
      60 63 72 75 10 60 63 72 78 10
      63 72 81 84 4 63 72 81 87 4
      66 63 72 75 4 66 63 72 78 4
      66 63 72 81 4 69 63 72 75 4
      69 63 72 78 4 69 63 72 81 4
      75 72 81 84 4 75 72 81 87 4
      75 72 81 90 10 78 72 81 84 4
      78 72 81 87 4 78 72 81 90 10
      84 81 90 93 9 87 81 90 93 9
      90 93 120 123 12 93 96 102 105 12
      96 93 120 123 12 99 96 102 105 12
     105 102 108 111 12 105 102 108 114 12
     108 114 120 123 12 117 114 120 123 12
      96 108 -102 -105 13 93 114 -120 -123 13
%FLAG DIHEDRALS_WITHOUT_HYDROGEN
%FORMAT(10I8)
       0 12 27 30 2 0 12 57 45 3
       0 12 57 60 3 12 27 30 33 5
      12 27 30 42 5 12 57 -45 42 6
      12 57 45 48 6 12 57 60 63 7
      15 12 27 30 2 15 12 57 45 3
      15 12 57 60 3 27 12 57 45 3
      27 12 57 60 3 27 30 -42 45 8
      30 27 12 57 2 30 42 45 48 5
      30 42 -45 57 5 33 30 42 45 8
      42 45 57 60 6 45 57 60 63 7
      48 45 57 60 6 57 60 63 72 9
      60 63 72 81 4 63 72 81 90 4
      72 81 90 93 9 81 90 93 96 11
      81 90 93 120 11 90 93 96 99 12
      90 93 96 102 12 90 93 120 114 12
      93 96 102 108 12 93 120 -114 108 12
      93 120 114 117 12 96 93 120 114 12
      96 102 108 111 12 96 102 -108 114 12
      99 96 93 120 12 99 96 102 108 12
     102 96 93 120 12 102 108 114 117 12
     102 108 -114 120 12 111 108 114 117 12
     111 108 114 120 12 27 42 -30 -33 13
      42 48 -45 -57 13 96 120 -93 -90 13
      93 102 -96 -99 13 102 114 -108 -111 13
     108 120 -114 -117 13
%FLAG EXCLUDED_ATOMS_LIST
%FORMAT(10I8)
       2 3 4 5 6 7 8 9 10 11
      16 20 21 3 4 5 6 10 20 4
       5 6 10 20 5 6 10 20 6 7
       8 9 10 11 12 15 16 17 20 21
      22 7 8 9 10 11 16 20 21 8
       9 10 20 9 10 20 10 20 11 12
      13 14 15 16 20 21 12 13 14 15
      16 17 20 13 14 15 16 14 15 15
      16 17 18 19 20 21 17 18 19 20
      21 22 18 19 20 21 19 20 20 21
      22 23 24 25 22 23 24 25 26 27
      28 23 24 25 26 27 28 29 30 31
      24 25 26 27 28 25 26 27 28 26
      27 28 29 30 31 32 27 28 29 30
      31 28 29 30 31 29 30 31 32 33
      41 30 31 32 31 32 32 33 34 35
      39 41 42 33 34 35 36 37 39 40
      41 42 34 35 36 37 38 39 41 42
      35 36 37 41 36 37 38 39 40 41
      37 38 39 38 39 40 41 42 39 40
      41 40 41 42 41 42 42 0
%FLAG HBOND_ACOEF
%FORMAT(5E16.8)

%FLAG HBOND_BCOEF
%FORMAT(5E16.8)

%FLAG HBCUT
%FORMAT(5E16.8)

%FLAG AMBER_ATOM_TYPE
%FORMAT(20a4)
c3 hc hc hc c3 c3 hc hc hc n2 ce nh hn hn ne c2 nh hn hn nh
os c3 h1 h1 c3 hc hc c3 h1 h1 os ca ca cl ca ha ca cl ca cl
ca ha
%FLAG TREE_CHAIN_CLASSIFICATION
%FORMAT(20a4)
M E E E M 3 E E E S B B E E S S B E E M
M M E E M E E M E E M M B E B E B E S E
M E
%FLAG JOIN_ARRAY
%FORMAT(10I8)
       0 0 0 0 0 0 0 0 0 0
       0 0 0 0 0 0 0 0 0 0
       0 0 0 0 0 0 0 0 0 0
       0 0 0 0 0 0 0 0 0 0
       0 0
%FLAG IROTAT
%FORMAT(10I8)
       0 0 0 0 0 0 0 0 0 0
       0 0 0 0 0 0 0 0 0 0
       0 0 0 0 0 0 0 0 0 0
       0 0 0 0 0 0 0 0 0 0
       0 0
%FLAG RADIUS_SET
%FORMAT(1a80)
modified Bondi radii (mbondi)
%FLAG RADII
%FORMAT(5E16.8)
  1.70000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00
  1.70000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.55000000E+00
  1.70000000E+00 1.55000000E+00 1.30000000E+00 1.30000000E+00 1.55000000E+00
  1.70000000E+00 1.55000000E+00 1.30000000E+00 1.30000000E+00 1.55000000E+00
  1.50000000E+00 1.70000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00
  1.30000000E+00 1.30000000E+00 1.70000000E+00 1.30000000E+00 1.30000000E+00
  1.50000000E+00 1.70000000E+00 1.70000000E+00 1.70000000E+00 1.70000000E+00
  1.30000000E+00 1.70000000E+00 1.70000000E+00 1.70000000E+00 1.70000000E+00
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%FLAG SCREEN
%FORMAT(5E16.8)
  7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01
  7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.90000000E-01
  7.20000000E-01 7.90000000E-01 8.50000000E-01 8.50000000E-01 7.90000000E-01
  7.20000000E-01 7.90000000E-01 8.50000000E-01 8.50000000E-01 7.90000000E-01
  8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01
  8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01
  8.50000000E-01 7.20000000E-01 7.20000000E-01 8.00000000E-01 7.20000000E-01
  8.50000000E-01 7.20000000E-01 8.00000000E-01 7.20000000E-01 8.00000000E-01
  7.20000000E-01 8.50000000E-01

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