AMBER: PARAMETERISATION PROBLEM

From: Claire Zerafa <cporteli.waldonet.net.mt>
Date: Wed, 06 Sep 2006 14:12:04 +0000

Hi Dear All,

I generated two molecules in Ligbuilder I attach the pdb files for
both in the email. I parameterised these using antechamber, and
generated a prepin and frcmod file for each one. Then I tried to read
them into xleap to generate prmtop and inpcrd files. I had a problem in
that after reading the prepin and frcmod files, xleap aborted giving the
same error message in each case:

octane2 4% $AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99
-I: Adding /usr/local/amber8/dat/leap/prep to search path.
-I: Adding /usr/local/amber8/dat/leap/lib to search path.
-I: Adding /usr/local/amber8/dat/leap/parm to search path.
-I: Adding /usr/local/amber8/dat/leap/cmd to search path.
-s: Ignoring startup file: leaprc
-f: Source /usr/local/amber8/dat/leap/cmd/leaprc.ff99.
!FATAL ERROR----------------------------------------
!FATAL: In file [atom.c], line 444
!FATAL: Message: bondAtomProblem found
!
!ABORTING.
octane2 5%


I'm not quite sure what the error is....

I would appreciate some tips..

Thanks

Claire


    0 0 2

This is a remark line
molecule.res
 C1 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 C4 ce M 3 2 1 1.540 111.208 180.000 -0.21059
   5 H5 ha E 4 3 2 1.088 165.197 -120.716 0.16187
   6 C3 c M 4 3 2 1.438 69.138 9.771 0.55808
   7 O20 o E 6 4 3 1.220 126.584 168.124 -0.49835
   8 C2 c3 M 6 4 3 1.504 113.437 -11.850 -0.18203
   9 H4 hc E 8 6 4 1.100 109.240 -66.039 0.07864
  10 H3 hc E 8 6 4 1.099 109.559 173.883 0.08603
  11 C1 c3 M 8 6 4 1.514 109.891 53.555 -0.04964
  12 H2 hc E 11 8 6 1.099 108.451 -176.978 0.05688
  13 H1 hc E 11 8 6 1.100 108.411 64.200 0.06988
  14 C10 cf M 11 8 6 1.541 111.377 -56.973 -0.01150
  15 C5 cf M 14 11 8 1.488 114.224 32.303 -0.03985
  16 C6 c3 M 15 14 11 1.520 118.564 178.040 -0.05149
  17 H7 hc E 16 15 14 1.100 109.038 92.255 0.06430
  18 H6 hc E 16 15 14 1.100 109.047 -148.312 0.07051
  19 C7 c3 M 16 15 14 1.512 111.344 -28.012 -0.07301
  20 H9 hc E 19 16 15 1.099 109.559 177.155 0.05060
  21 H8 hc E 19 16 15 1.100 109.537 -62.719 0.05672
  22 C8 c3 M 19 16 15 1.540 109.083 57.213 -0.00947
  23 H10 hc E 22 19 16 1.100 108.753 60.696 0.07357
  24 C9 ce M 22 19 16 1.543 110.261 -58.582 -0.11717
  25 C11 ce M 24 22 19 1.463 116.228 -151.201 -0.04760
  26 H11 ha E 25 24 22 1.089 118.011 -179.102 0.14502
  27 C12 c2 M 25 24 22 1.346 123.967 0.961 -0.23121
  28 H12 ha E 27 25 24 1.089 119.355 179.973 0.12593
  29 C13 c3 M 27 25 24 1.519 121.349 -0.077 0.01524
  30 C18 c2 B 29 27 25 1.502 107.051 -94.266 -0.25082
  31 H18 ha E 30 29 27 1.090 118.524 -135.022 0.13355
  32 C20 ce B 30 29 27 1.337 120.718 45.040 -0.07239
  33 C21 ce B 32 30 29 1.470 120.721 179.988 -0.16788
  34 H ha E 33 32 30 1.088 117.814 -165.017 0.14809
  35 C22 c2 B 33 32 30 1.339 118.915 14.976 -0.17135
  36 H26 ha E 35 33 32 1.090 120.464 -0.022 0.10309
  37 H24 ha E 35 33 32 1.089 121.707 -179.945 0.13914
  38 H22 ha E 32 30 29 1.090 120.758 -0.064 0.14006
  39 C14 c3 M 29 27 25 1.533 108.343 26.753 -0.05234
  40 H13 hc E 39 29 27 1.100 108.896 61.367 0.06990
  41 C15 c3 M 39 29 27 1.541 103.956 176.291 -0.07440
  42 H15 hc E 41 39 29 1.099 111.347 86.853 0.06758
  43 H14 hc E 41 39 29 1.100 111.345 -150.642 0.07839
  44 C16 c3 M 41 39 29 1.532 101.923 -31.946 -0.09309
  45 H17 hc E 44 41 39 1.101 109.925 120.862 0.05714
  46 H16 hc E 44 41 39 1.100 109.946 -118.567 0.06962
  47 C17 c3 M 44 41 39 1.555 107.636 1.185 0.10695
  48 H19 hx E 47 44 41 1.100 112.135 -89.584 0.10146
  49 N n4 M 47 44 41 1.540 107.745 149.080 -0.80145
  50 H21 hn E 49 47 44 1.100 109.530 -18.950 0.45887
  51 H23 hn E 49 47 44 1.101 109.423 -138.918 0.46272
  52 C19 c3 M 49 47 44 1.540 109.470 101.105 0.32611
  53 H25 hx E 52 49 47 1.088 109.457 179.983 0.13219
  54 H20 hx E 52 49 47 1.088 109.471 -60.064 0.10312
  55 O3 oh M 52 49 47 1.430 109.502 59.977 -0.54970
  56 H27 ho E 55 52 49 0.969 109.994 -179.968 0.44411


LOOP
   C5 C4
   C9 C10
  C14 C8
  C17 C13

IMPROPER
   C3 C5 C4 H5
   C2 C4 C3 O20
   C1 C9 C10 C5
   C6 C4 C5 C10
   C8 C11 C9 C10
  C12 C9 C11 H11
  C13 C11 C12 H12
  C13 C20 C18 H18
  C18 C21 C20 H22
  C22 C20 C21 H
  C21 H26 C22 H24

DONE
STOP


remark goes here
MASS

BOND

ANGLE
ce-cf-c3 64.300 122.890 same as c2-cf-c3
c3-c3-cf 63.700 110.960 same as c2-c3-c3
cf-ce-c3 64.300 122.890 same as c2-ce-c3
c3-c3-ce 63.700 110.960 same as c2-c3-c3
n4-c3-oh 68.811 112.200 Calculated with empirical approach
hx-c3-oh 42.012 110.910 Calculated with empirical approach

DIHE
ce-cf-c3-hc 1 0.000 0.000 2.000 same as X -c2-c3-X
ce-cf-c3-c3 1 0.000 0.000 2.000 same as X -c2-c3-X
c3-c3-cf-cf 1 0.000 0.000 2.000 same as X -c2-c3-X
hc-c3-cf-cf 1 0.000 0.000 2.000 same as X -c2-c3-X
cf-ce-c3-c3 1 0.000 0.000 2.000 same as X -c2-c3-X
cf-ce-c3-hc 1 0.000 0.000 2.000 same as X -c2-c3-X
c3-c3-ce-ce 1 0.000 0.000 2.000 same as X -c2-c3-X
hc-c3-ce-ce 1 0.000 0.000 2.000 same as X -c2-c3-X

IMPROPER

NONBON





remark goes here
MASS

BOND

ANGLE
c3-ce-cf 65.700 117.400 same as c3-c2-cf
c3-c3-ce 63.700 110.960 same as c2-c3-c3
na-cd-oh 74.302 111.830 Calculated with empirical approach

DIHE
hc-c3-ce-cf 1 0.000 0.000 2.000 same as X -c2-c3-X
hc-c3-ce-ce 1 0.000 0.000 2.000 same as X -c2-c3-X
c3-c3-ce-cf 1 0.000 0.000 2.000 same as X -c2-c3-X
c3-c3-ce-ce 1 0.000 0.000 2.000 same as X -c2-c3-X
cc-cd-oh-ho 1 1.050 180.000 2.000 same as X -c2-oh-X
na-cd-oh-ho 1 1.050 180.000 2.000 same as X -c2-oh-X

IMPROPER

NONBON





    0 0 2

This is a remark line
molecule.res
 C2 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 C6 c3 M 3 2 1 1.540 111.208 180.000 -0.06072
   5 H4 hc E 4 3 2 1.100 82.216 133.476 0.06816
   6 H22 hc E 4 3 2 1.084 64.250 -110.439 0.06217
   7 C1 c3 M 4 3 2 1.396 66.531 17.402 -0.07268
   8 H1 hc E 7 4 3 1.100 111.224 -72.651 0.04889
   9 H8 hc E 7 4 3 1.100 109.525 49.425 0.04929
  10 C2 c3 M 7 4 3 1.397 118.206 178.815 -0.18176
  11 H3 hc E 10 7 4 1.100 92.897 115.520 0.07003
  12 H27 hc E 10 7 4 1.100 110.541 -131.334 0.07352
  13 C21 c M 10 7 4 1.393 121.568 -0.168 0.56739
  14 O9 o E 13 10 7 1.220 120.034 -179.592 -0.53561
  15 C22 cf M 13 10 7 1.416 119.813 0.710 -0.25634
  16 H23 ha E 15 13 10 1.090 121.019 177.901 0.15132
  17 C5 ce M 15 13 10 1.411 118.975 -0.848 -0.00232
  18 C3 ce M 17 15 13 1.470 120.390 -179.066 -0.05689
  19 C12 c2 B 18 17 15 1.338 121.738 -60.508 -0.18338
  20 H28 ha E 19 18 17 1.089 123.283 0.006 0.12127
  21 H21 ha E 19 18 17 1.092 118.958 179.996 0.12145
  22 C17 ce M 18 17 15 1.471 117.777 119.471 -0.03939
  23 C11 c2 B 22 18 17 1.338 121.731 -59.991 -0.20275
  24 H ha E 23 22 18 1.090 123.294 0.050 0.11957
  25 H20 ha E 23 22 18 1.091 118.952 -179.998 0.12207
  26 C18 ce M 22 18 17 1.470 117.767 120.031 -0.15268
  27 H6 ha E 26 22 18 1.090 117.873 75.003 0.12694
  28 C7 c2 M 26 22 18 1.339 121.661 -105.049 -0.07637
  29 C15 c3 3 28 26 22 1.509 123.299 0.053 -0.05552
  30 C10 c3 3 29 28 26 1.541 109.305 120.395 -0.06915
  31 H15 hc E 30 29 28 1.088 109.417 -149.984 0.03726
  32 H26 hc E 30 29 28 1.087 109.464 89.973 0.03017
  33 C16 c3 3 30 29 28 1.526 109.467 -30.018 -0.09455
  34 H25 hc E 33 30 29 1.089 109.416 60.004 0.04027
  35 H19 hc E 33 30 29 1.088 109.476 -59.934 0.03227
  36 H12 hc E 33 30 29 1.088 109.478 179.998 0.03061
  37 H13 hc E 29 28 26 1.101 109.334 -120.661 0.06425
  38 H2 hc E 29 28 26 1.100 112.362 -0.085 0.04895
  39 C13 c3 M 28 26 22 1.501 118.919 179.997 -0.04016
  40 H24 hc E 39 28 26 1.089 109.471 -14.905 0.04601
  41 H16 hc E 39 28 26 1.088 109.490 -134.983 0.03588
  42 C8 c3 M 39 28 26 1.526 109.462 105.035 0.01767
  43 H7 hc E 42 39 28 1.088 109.503 -179.954 0.05290
  44 C20 c3 3 42 39 28 1.527 109.470 -59.962 -0.08784
  45 H11 hc E 44 42 39 1.088 109.441 -60.013 0.03051
  46 H10 hc E 44 42 39 1.088 109.449 59.975 0.04276
  47 H9 hc E 44 42 39 1.088 109.463 179.980 0.04261
  48 C9 cc M 42 39 28 1.501 109.476 60.032 -0.16161
  49 C19 cc M 48 42 39 1.470 127.062 -119.985 -0.17438
  50 H17 ha E 49 48 42 1.090 127.011 0.032 0.15557
  51 C4 cd M 49 48 42 1.334 105.467 179.984 -0.16612
  52 H5 h4 E 51 49 48 1.090 125.823 179.907 0.16683
  53 N1 na M 51 49 48 1.302 107.627 0.002 -0.18357
  54 H14 hn E 53 51 49 1.032 123.059 179.975 0.29974
  55 C14 cd M 53 51 49 1.301 113.852 -0.024 0.04107
  56 O oh M 55 53 51 1.501 126.572 -179.989 -0.48525
  57 H18 ho E 56 55 53 1.100 109.485 18.334 0.42161


LOOP
   C5 C6
  C14 C9

IMPROPER
   C2 C22 C21 O9
  C21 C5 C22 H23
   C6 C3 C5 C22
  C12 C5 C3 C17
   C3 H28 C12 H21
  C11 C3 C17 C18
  C17 H C11 H20
   C7 C17 C18 H6
  C15 C13 C7 C18
   C8 C19 C9 C14
   C9 C4 C19 H17
  C19 H5 C4 N1
   C4 C14 N1 H14
   C9 N1 C14 O

DONE
STOP


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Received on Sun Sep 10 2006 - 06:07:04 PDT
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