Dear Amber folk,
I'm running into trouble trying to construct a complex using parameters for
a ligand contained in a custom .lib file that I have created. When I try to
produce the complex, it treat the protein fine, but seems unable to link the
information in my custom .lib file to the ligand atoms in the PDB I'm giving
tleap.
The ligands I am using are made up of multiple sugar rings in a chain - and
for the purposes of post MD/MC analysis, I'd want to be able to treat each
ring as a separate residue. This means I would be able to use idecomp to
look at protein-ligand terms on a per ring basis. To achieve this, I did the
following:
1. Take ligand in PDB format and generate .mol2 file using antechamber -
charges come from RESP using GAMESS. At this point, the ligand is being
treated as a single residue to get the charges as antechamber cannot handle
multiple residues (correct?). I'm aware that I could be parametrising each
ring separately and then linking them together. I've not tired this (it
seems like a lot more work!) and you could argue that the charges you get
are not as representative as those when you do the RESP calculation on the
whole ligand.
2. Edit the .mol2 file to split the ligand into rings and cap e.g.
.<TRIPOS>MOLECULE
LIG
90 92 1 0 0
becomes...
.<TRIPOS>MOLECULE
LIG
90 92 4 0 0
I have changed the 9th column in each .<TRIPOS>ATOM line to be the residue
name for that ring. Finally at the bottom, I have changed what was there
into:
.<TRIPOS>SUBSTRUCTURE
1 OME 1 RESIDUE
2 NAG 6 RESIDUE
...etc
3. Use tleap to load in the modified .mol2 file (no errors) and save it as a
.lib
LIG=loadmol2 Siaa_6Galb_4GlNb.mol2
check LIG (comes back fine apart from it being -1 charge, which it should
be!)
saveoff LIG Siaa_6Galb_4GlNb.lib
4. Try to produce the complex:
source leaprc.ff99SB
loadoff Siaa_6Galb_4GlNb.lib
COMPLEX=loadpdb complex.pdb
saveamberparm COMPLEX complex.prmtop complex.inpcrd
This is where the problems occur. Here is my leap output - I've attached it
from the loadoff command in full below, sorry for the length!
The first place I think there could be an issue is here:
...
(Residue 252: THR, Nonterminal, was not found in name map.)
Mapped residue SER, term: Terminal/last, seq. number: 253 to: CSER.
(Residue 254: OME, Terminal/beginning, was not found in name map.)
(Residue 255: NAG, Nonterminal, was not found in name map.)
Unknown residue: NAG number: 255 type: Nonterminal
(Residue 256: GAL, Nonterminal, was not found in name map.)
Unknown residue: GAL number: 256 type: Nonterminal
(Residue 257: SIA, Terminal/last, was not found in name map.)
Unknown residue: SIA number: 257 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
<JOINING STARTS HERE>
It seems that residues are just not being loaded from the .lib file
properly, or I'm putting them into the PDB incorrectly. Here is the relevent
part of the PDB:
...
ATOM 3912 O SER 254 49.660 95.870 56.710 1.00
ATOM 3913 OXT SER 254 50.970 97.660 56.880 1.00
TER
ATOM 3914 CH3 OME B 255 103.680 65.440 88.080 1.00
ATOM 3915 H1 OME B 255 103.880 64.460 88.510 1.00
ATOM 3916 H2 OME B 255 103.650 65.400 86.990 1.00
ATOM 3917 H12 OME B 255 104.560 66.060 88.310 1.00
ATOM 3918 O OME B 255 102.530 66.010 88.600 1.00
ATOM 3919 C1 NAG B 256 101.820 66.980 87.890 1.00
ATOM 3920 H10 NAG B 256 101.600 66.510 86.930 1.00
ATOM 3921 O5 NAG B 256 102.500 68.200 87.880 1.00
ATOM 3922 C5 NAG B 256 101.820 69.280 87.390 1.00
ATOM 3923 H5 NAG B 256 101.410 69.090 86.400 1.00
ATOM 3924 C6 NAG B 256 102.890 70.390 87.180 1.00
ATOM 3925 H61 NAG B 256 103.600 70.100 86.400 1.00
ATOM 3926 H62 NAG B 256 102.300 71.250 86.880 1.00
ATOM 3927 O6 NAG B 256 103.600 70.690 88.440 1.00
ATOM 3928 H6O NAG B 256 104.180 69.940 88.570 1.00
ATOM 3929 C2 NAG B 256 100.440 67.230 88.550 1.00
ATOM 3930 H14 NAG B 256 100.600 67.210 89.620 1.00
ATOM 3931 N2 NAG B 256 99.600 66.120 88.230 1.00
ATOM 3932 H2N NAG B 256 99.650 65.820 87.260 1.00
ATOM 3933 C2N NAG B 256 98.920 65.320 89.030 1.00
ATOM 3934 O2N NAG B 256 98.920 65.380 90.290 1.00
ATOM 3935 CME NAG B 256 98.170 64.200 88.380 1.00
ATOM 3936 H1M NAG B 256 98.630 63.260 88.680 1.00
ATOM 3937 H2M NAG B 256 98.280 64.210 87.290 1.00
ATOM 3938 H3M NAG B 256 97.150 64.120 88.760 1.00
ATOM 3939 C3 NAG B 256 99.720 68.520 88.160 1.00
ATOM 3940 H13 NAG B 256 99.360 68.560 87.130 1.00
ATOM 3941 O3 NAG B 256 98.590 68.630 89.030 1.00
ATOM 3942 H3O NAG B 256 98.060 69.400 88.790 1.00
ATOM 3943 C4 NAG B 256 100.690 69.670 88.300 1.00
ATOM 3944 H4 NAG B 256 101.020 69.660 89.340 1.00
ATOM 3945 O4 NAG B 256 100.250 70.980 87.900 1.00
ATOM 3946 C10 GAL B 257 99.580 71.770 88.910 1.00
ATOM 3947 H11 GAL B 257 100.050 71.570 89.870 1.00
ATOM 3948 O10 GAL B 257 98.160 71.600 88.930 1.00
ATOM 3949 C20 GAL B 257 99.840 73.250 88.500 1.00
ATOM 3950 H16 GAL B 257 99.180 73.620 87.720 1.00
ATOM 3951 O2 GAL B 257 101.180 73.390 88.010 1.00
ATOM 3952 H2O GAL B 257 101.490 72.490 87.900 1.00
ATOM 3953 C18 GAL B 257 99.500 74.020 89.730 1.00
ATOM 3954 H15 GAL B 257 100.190 73.630 90.480 1.00
ATOM 3955 O13 GAL B 257 99.680 75.400 89.450 1.00
ATOM 3956 H23 GAL B 257 99.120 75.680 88.720 1.00
ATOM 3957 C16 GAL B 257 98.030 73.730 90.130 1.00
ATOM 3958 H21 GAL B 257 97.770 74.300 91.020 1.00
ATOM 3959 O14 GAL B 257 97.270 74.440 89.110 1.00
ATOM 3960 H4O GAL B 257 96.530 74.900 89.530 1.00
ATOM 3961 C12 GAL B 257 97.580 72.250 90.120 1.00
ATOM 3962 H17 GAL B 257 97.920 71.830 91.060 1.00
ATOM 3963 C14 GAL B 257 96.110 71.930 90.050 1.00
ATOM 3964 H19 GAL B 257 95.580 72.790 90.460 1.00
ATOM 3965 H20 GAL B 257 95.850 71.800 89.000 1.00
ATOM 3966 O11 GAL B 257 95.860 70.660 90.760 1.00
ATOM 3967 C21 GAL B 257 94.810 69.860 90.120 1.00
ATOM 3968 C11 SIA B 258 93.480 70.720 90.190 1.00
ATOM 3969 O1A SIA B 258 93.090 71.280 89.110 1.00
ATOM 3970 O1B SIA B 258 92.810 70.700 91.230 1.00
ATOM 3971 C19 SIA B 258 94.650 68.650 91.040 1.00
ATOM 3972 H3A SIA B 258 95.660 68.260 91.170 1.00
ATOM 3973 H3E SIA B 258 94.320 68.880 92.050 1.00
ATOM 3974 C17 SIA B 258 93.780 67.520 90.470 1.00
ATOM 3975 H22 SIA B 258 92.750 67.870 90.450 1.00
ATOM 3976 O15 SIA B 258 93.880 66.390 91.290 1.00
ATOM 3977 H27 SIA B 258 94.770 66.030 91.320 1.00
ATOM 3978 C13 SIA B 258 94.220 67.120 89.080 1.00
ATOM 3979 H18 SIA B 258 95.100 66.480 89.150 1.00
ATOM 3980 N5 SIA B 258 93.160 66.280 88.460 1.00
ATOM 3981 H5N SIA B 258 92.390 66.780 88.050 1.00
ATOM 3982 C5N SIA B 258 93.250 64.970 88.100 1.00
ATOM 3983 O5N SIA B 258 93.870 64.060 88.630 1.00
ATOM 3984 C22 SIA B 258 92.430 64.700 86.850 1.00
ATOM 3985 H24 SIA B 258 92.130 63.650 86.820 1.00
ATOM 3986 H25 SIA B 258 91.540 65.330 86.830 1.00
ATOM 3987 H26 SIA B 258 93.050 64.930 85.980 1.00
ATOM 3988 O12 SIA B 258 95.280 69.300 88.920 1.00
ATOM 3989 C15 SIA B 258 94.500 68.310 88.190 1.00
ATOM 3990 H6 SIA B 258 93.540 68.720 87.880 1.00
ATOM 3991 C7 SIA B 258 95.410 67.860 87.010 1.00
ATOM 3992 H7 SIA B 258 94.910 67.190 86.300 1.00
ATOM 3993 O7 SIA B 258 96.550 67.150 87.500 1.00
ATOM 3994 H7O SIA B 258 97.090 67.690 88.090 1.00
ATOM 3995 C8 SIA B 258 96.020 68.950 86.150 1.00
ATOM 3996 H8 SIA B 258 96.750 69.550 86.700 1.00
ATOM 3997 O8 SIA B 258 94.940 69.820 85.770 1.00
ATOM 3998 H8O SIA B 258 94.730 70.370 86.530 1.00
ATOM 3999 C9 SIA B 258 96.700 68.310 84.870 1.00
ATOM 4000 H9R SIA B 258 95.950 67.910 84.180 1.00
ATOM 4001 H9S SIA B 258 97.290 67.510 85.310 1.00
ATOM 4002 O9 SIA B 258 97.550 69.240 84.170 1.00
ATOM 4003 H9O SIA B 258 98.300 68.720 83.870 1.00
TER
I'm really at a bit of a loss as to what the issue could be. Is the way I'm
editing the .mol2 file for the ligand, breaking it into residues incorrect?
Should I have 'TER's between the rings in the PDB?
Any help would be greatly appriciated!
Many thanks,
Chris
START OF FULL tleap OUTPUT:
--------------------------------------------------------------------------------------------------
>
> loadoff Siaa_6Galb_4GlNb.lib
Loading library: ./Siaa_6Galb_4GlNb.lib
Loading: LIG
> COMPLEX=loadpdb original.pdb
Loading PDB file: ./original.pdb
Enter zPdbReadScan from call depth 0.
Exit zPdbReadScan from call depth 0.
Matching PDB residue names to LEaP variables.
Mapped residue LYS, term: Terminal/beginning, seq. number: 0 to: NLYS.
(Residue 1: HIE, Nonterminal, was not found in name map.)
(Residue 2: ASN, Nonterminal, was not found in name map.)
(Residue 3: GLY, Nonterminal, was not found in name map.)
(Residue 4: LYS, Nonterminal, was not found in name map.)
(Residue 5: LEU, Nonterminal, was not found in name map.)
(Residue 6: CYX, Nonterminal, was not found in name map.)
(Residue 7: LYS, Nonterminal, was not found in name map.)
(Residue 8: LEU, Nonterminal, was not found in name map.)
(Residue 9: ARG, Nonterminal, was not found in name map.)
(Residue 10: GLY, Nonterminal, was not found in name map.)
(Residue 11: VAL, Nonterminal, was not found in name map.)
(Residue 12: ALA, Nonterminal, was not found in name map.)
(Residue 13: PRO, Nonterminal, was not found in name map.)
(Residue 14: LEU, Nonterminal, was not found in name map.)
(Residue 15: HIE, Nonterminal, was not found in name map.)
(Residue 16: LEU, Nonterminal, was not found in name map.)
(Residue 17: GLY, Nonterminal, was not found in name map.)
(Residue 18: LYS, Nonterminal, was not found in name map.)
(Residue 19: CYX, Nonterminal, was not found in name map.)
(Residue 20: ASN, Nonterminal, was not found in name map.)
(Residue 21: ILE, Nonterminal, was not found in name map.)
(Residue 22: ALA, Nonterminal, was not found in name map.)
(Residue 23: GLY, Nonterminal, was not found in name map.)
(Residue 24: TRP, Nonterminal, was not found in name map.)
(Residue 25: ILE, Nonterminal, was not found in name map.)
(Residue 26: LEU, Nonterminal, was not found in name map.)
(Residue 27: GLY, Nonterminal, was not found in name map.)
(Residue 28: ASN, Nonterminal, was not found in name map.)
(Residue 29: PRO, Nonterminal, was not found in name map.)
(Residue 30: GLU, Nonterminal, was not found in name map.)
(Residue 31: CYX, Nonterminal, was not found in name map.)
(Residue 32: GLU, Nonterminal, was not found in name map.)
(Residue 33: SER, Nonterminal, was not found in name map.)
(Residue 34: LEU, Nonterminal, was not found in name map.)
(Residue 35: SER, Nonterminal, was not found in name map.)
(Residue 36: THR, Nonterminal, was not found in name map.)
(Residue 37: ALA, Nonterminal, was not found in name map.)
(Residue 38: SER, Nonterminal, was not found in name map.)
(Residue 39: SER, Nonterminal, was not found in name map.)
(Residue 40: TRP, Nonterminal, was not found in name map.)
(Residue 41: SER, Nonterminal, was not found in name map.)
(Residue 42: TYR, Nonterminal, was not found in name map.)
(Residue 43: ILE, Nonterminal, was not found in name map.)
(Residue 44: VAL, Nonterminal, was not found in name map.)
(Residue 45: GLU, Nonterminal, was not found in name map.)
(Residue 46: THR, Nonterminal, was not found in name map.)
(Residue 47: SER, Nonterminal, was not found in name map.)
(Residue 48: SER, Nonterminal, was not found in name map.)
(Residue 49: SER, Nonterminal, was not found in name map.)
(Residue 50: ASP, Nonterminal, was not found in name map.)
(Residue 51: ASN, Nonterminal, was not found in name map.)
(Residue 52: GLY, Nonterminal, was not found in name map.)
(Residue 53: THR, Nonterminal, was not found in name map.)
(Residue 54: CYX, Nonterminal, was not found in name map.)
(Residue 55: TYR, Nonterminal, was not found in name map.)
(Residue 56: PRO, Nonterminal, was not found in name map.)
(Residue 57: GLY, Nonterminal, was not found in name map.)
(Residue 58: ASP, Nonterminal, was not found in name map.)
(Residue 59: PHE, Nonterminal, was not found in name map.)
(Residue 60: ILE, Nonterminal, was not found in name map.)
(Residue 61: ASP, Nonterminal, was not found in name map.)
(Residue 62: TYR, Nonterminal, was not found in name map.)
(Residue 63: GLU, Nonterminal, was not found in name map.)
(Residue 64: GLU, Nonterminal, was not found in name map.)
(Residue 65: LEU, Nonterminal, was not found in name map.)
(Residue 66: ARG, Nonterminal, was not found in name map.)
(Residue 67: GLU, Nonterminal, was not found in name map.)
(Residue 68: GLN, Nonterminal, was not found in name map.)
(Residue 69: LEU, Nonterminal, was not found in name map.)
(Residue 70: SER, Nonterminal, was not found in name map.)
(Residue 71: SER, Nonterminal, was not found in name map.)
(Residue 72: VAL, Nonterminal, was not found in name map.)
(Residue 73: SER, Nonterminal, was not found in name map.)
(Residue 74: SER, Nonterminal, was not found in name map.)
(Residue 75: PHE, Nonterminal, was not found in name map.)
(Residue 76: GLU, Nonterminal, was not found in name map.)
(Residue 77: ARG, Nonterminal, was not found in name map.)
(Residue 78: PHE, Nonterminal, was not found in name map.)
(Residue 79: GLU, Nonterminal, was not found in name map.)
(Residue 80: ILE, Nonterminal, was not found in name map.)
(Residue 81: PHE, Nonterminal, was not found in name map.)
(Residue 82: PRO, Nonterminal, was not found in name map.)
(Residue 83: LYS, Nonterminal, was not found in name map.)
(Residue 84: THR, Nonterminal, was not found in name map.)
(Residue 85: SER, Nonterminal, was not found in name map.)
(Residue 86: SER, Nonterminal, was not found in name map.)
(Residue 87: TRP, Nonterminal, was not found in name map.)
(Residue 88: PRO, Nonterminal, was not found in name map.)
(Residue 89: ASN, Nonterminal, was not found in name map.)
(Residue 90: HIE, Nonterminal, was not found in name map.)
(Residue 91: ASP, Nonterminal, was not found in name map.)
(Residue 92: SER, Nonterminal, was not found in name map.)
(Residue 93: ASN, Nonterminal, was not found in name map.)
(Residue 94: LYS, Nonterminal, was not found in name map.)
(Residue 95: GLY, Nonterminal, was not found in name map.)
(Residue 96: VAL, Nonterminal, was not found in name map.)
(Residue 97: THR, Nonterminal, was not found in name map.)
(Residue 98: ALA, Nonterminal, was not found in name map.)
(Residue 99: ALA, Nonterminal, was not found in name map.)
(Residue 100: CYX, Nonterminal, was not found in name map.)
(Residue 101: PRO, Nonterminal, was not found in name map.)
(Residue 102: HIE, Nonterminal, was not found in name map.)
(Residue 103: ALA, Nonterminal, was not found in name map.)
(Residue 104: GLY, Nonterminal, was not found in name map.)
(Residue 105: ALA, Nonterminal, was not found in name map.)
(Residue 106: LYS, Nonterminal, was not found in name map.)
(Residue 107: SER, Nonterminal, was not found in name map.)
(Residue 108: PHE, Nonterminal, was not found in name map.)
(Residue 109: TYR, Nonterminal, was not found in name map.)
(Residue 110: LYS, Nonterminal, was not found in name map.)
(Residue 111: ASN, Nonterminal, was not found in name map.)
(Residue 112: LEU, Nonterminal, was not found in name map.)
(Residue 113: ILE, Nonterminal, was not found in name map.)
(Residue 114: TRP, Nonterminal, was not found in name map.)
(Residue 115: LEU, Nonterminal, was not found in name map.)
(Residue 116: VAL, Nonterminal, was not found in name map.)
(Residue 117: LYS, Nonterminal, was not found in name map.)
(Residue 118: LYS, Nonterminal, was not found in name map.)
(Residue 119: GLY, Nonterminal, was not found in name map.)
(Residue 120: ASN, Nonterminal, was not found in name map.)
(Residue 121: SER, Nonterminal, was not found in name map.)
(Residue 122: TYR, Nonterminal, was not found in name map.)
(Residue 123: PRO, Nonterminal, was not found in name map.)
(Residue 124: LYS, Nonterminal, was not found in name map.)
(Residue 125: LEU, Nonterminal, was not found in name map.)
(Residue 126: SER, Nonterminal, was not found in name map.)
(Residue 127: LYS, Nonterminal, was not found in name map.)
(Residue 128: SER, Nonterminal, was not found in name map.)
(Residue 129: TYR, Nonterminal, was not found in name map.)
(Residue 130: ILE, Nonterminal, was not found in name map.)
(Residue 131: ASN, Nonterminal, was not found in name map.)
(Residue 132: ASP, Nonterminal, was not found in name map.)
(Residue 133: LYS, Nonterminal, was not found in name map.)
(Residue 134: GLY, Nonterminal, was not found in name map.)
(Residue 135: LYS, Nonterminal, was not found in name map.)
(Residue 136: GLU, Nonterminal, was not found in name map.)
(Residue 137: VAL, Nonterminal, was not found in name map.)
(Residue 138: LEU, Nonterminal, was not found in name map.)
(Residue 139: VAL, Nonterminal, was not found in name map.)
(Residue 140: LEU, Nonterminal, was not found in name map.)
(Residue 141: TRP, Nonterminal, was not found in name map.)
(Residue 142: GLY, Nonterminal, was not found in name map.)
(Residue 143: ILE, Nonterminal, was not found in name map.)
(Residue 144: HIE, Nonterminal, was not found in name map.)
(Residue 145: HIE, Nonterminal, was not found in name map.)
(Residue 146: PRO, Nonterminal, was not found in name map.)
(Residue 147: SER, Nonterminal, was not found in name map.)
(Residue 148: THR, Nonterminal, was not found in name map.)
(Residue 149: SER, Nonterminal, was not found in name map.)
(Residue 150: ALA, Nonterminal, was not found in name map.)
(Residue 151: ASP, Nonterminal, was not found in name map.)
(Residue 152: GLN, Nonterminal, was not found in name map.)
(Residue 153: GLN, Nonterminal, was not found in name map.)
(Residue 154: SER, Nonterminal, was not found in name map.)
(Residue 155: LEU, Nonterminal, was not found in name map.)
(Residue 156: TYR, Nonterminal, was not found in name map.)
(Residue 157: GLN, Nonterminal, was not found in name map.)
(Residue 158: ASN, Nonterminal, was not found in name map.)
(Residue 159: ALA, Nonterminal, was not found in name map.)
(Residue 160: ASP, Nonterminal, was not found in name map.)
(Residue 161: ALA, Nonterminal, was not found in name map.)
(Residue 162: TYR, Nonterminal, was not found in name map.)
(Residue 163: VAL, Nonterminal, was not found in name map.)
(Residue 164: PHE, Nonterminal, was not found in name map.)
(Residue 165: VAL, Nonterminal, was not found in name map.)
(Residue 166: GLY, Nonterminal, was not found in name map.)
(Residue 167: SER, Nonterminal, was not found in name map.)
(Residue 168: SER, Nonterminal, was not found in name map.)
(Residue 169: ARG, Nonterminal, was not found in name map.)
(Residue 170: TYR, Nonterminal, was not found in name map.)
(Residue 171: SER, Nonterminal, was not found in name map.)
(Residue 172: LYS, Nonterminal, was not found in name map.)
(Residue 173: LYS, Nonterminal, was not found in name map.)
(Residue 174: PHE, Nonterminal, was not found in name map.)
(Residue 175: LYS, Nonterminal, was not found in name map.)
(Residue 176: PRO, Nonterminal, was not found in name map.)
(Residue 177: GLU, Nonterminal, was not found in name map.)
(Residue 178: ILE, Nonterminal, was not found in name map.)
(Residue 179: ALA, Nonterminal, was not found in name map.)
(Residue 180: ILE, Nonterminal, was not found in name map.)
(Residue 181: ARG, Nonterminal, was not found in name map.)
(Residue 182: PRO, Nonterminal, was not found in name map.)
(Residue 183: LYS, Nonterminal, was not found in name map.)
(Residue 184: VAL, Nonterminal, was not found in name map.)
(Residue 185: ARG, Nonterminal, was not found in name map.)
(Residue 186: GLY, Nonterminal, was not found in name map.)
(Residue 187: GLN, Nonterminal, was not found in name map.)
(Residue 188: GLU, Nonterminal, was not found in name map.)
(Residue 189: GLY, Nonterminal, was not found in name map.)
(Residue 190: ARG, Nonterminal, was not found in name map.)
(Residue 191: MET, Nonterminal, was not found in name map.)
(Residue 192: ASN, Nonterminal, was not found in name map.)
(Residue 193: TYR, Nonterminal, was not found in name map.)
(Residue 194: TYR, Nonterminal, was not found in name map.)
(Residue 195: TRP, Nonterminal, was not found in name map.)
(Residue 196: THR, Nonterminal, was not found in name map.)
(Residue 197: LEU, Nonterminal, was not found in name map.)
(Residue 198: VAL, Nonterminal, was not found in name map.)
(Residue 199: GLU, Nonterminal, was not found in name map.)
(Residue 200: PRO, Nonterminal, was not found in name map.)
(Residue 201: GLY, Nonterminal, was not found in name map.)
(Residue 202: ASP, Nonterminal, was not found in name map.)
(Residue 203: LYS, Nonterminal, was not found in name map.)
(Residue 204: ILE, Nonterminal, was not found in name map.)
(Residue 205: THR, Nonterminal, was not found in name map.)
(Residue 206: PHE, Nonterminal, was not found in name map.)
(Residue 207: GLU, Nonterminal, was not found in name map.)
(Residue 208: ALA, Nonterminal, was not found in name map.)
(Residue 209: THR, Nonterminal, was not found in name map.)
(Residue 210: GLY, Nonterminal, was not found in name map.)
(Residue 211: ASN, Nonterminal, was not found in name map.)
(Residue 212: LEU, Nonterminal, was not found in name map.)
(Residue 213: VAL, Nonterminal, was not found in name map.)
(Residue 214: VAL, Nonterminal, was not found in name map.)
(Residue 215: PRO, Nonterminal, was not found in name map.)
(Residue 216: ARG, Nonterminal, was not found in name map.)
(Residue 217: TYR, Nonterminal, was not found in name map.)
(Residue 218: ALA, Nonterminal, was not found in name map.)
(Residue 219: PHE, Nonterminal, was not found in name map.)
(Residue 220: ALA, Nonterminal, was not found in name map.)
(Residue 221: MET, Nonterminal, was not found in name map.)
(Residue 222: GLU, Nonterminal, was not found in name map.)
(Residue 223: ARG, Nonterminal, was not found in name map.)
(Residue 224: ASN, Nonterminal, was not found in name map.)
(Residue 225: ALA, Nonterminal, was not found in name map.)
(Residue 226: GLY, Nonterminal, was not found in name map.)
(Residue 227: SER, Nonterminal, was not found in name map.)
(Residue 228: GLY, Nonterminal, was not found in name map.)
(Residue 229: ILE, Nonterminal, was not found in name map.)
(Residue 230: ILE, Nonterminal, was not found in name map.)
(Residue 231: ILE, Nonterminal, was not found in name map.)
(Residue 232: SER, Nonterminal, was not found in name map.)
(Residue 233: ASP, Nonterminal, was not found in name map.)
(Residue 234: THR, Nonterminal, was not found in name map.)
(Residue 235: PRO, Nonterminal, was not found in name map.)
(Residue 236: VAL, Nonterminal, was not found in name map.)
(Residue 237: HIE, Nonterminal, was not found in name map.)
(Residue 238: ASP, Nonterminal, was not found in name map.)
(Residue 239: CYX, Nonterminal, was not found in name map.)
(Residue 240: ASN, Nonterminal, was not found in name map.)
(Residue 241: THR, Nonterminal, was not found in name map.)
(Residue 242: THR, Nonterminal, was not found in name map.)
(Residue 243: CYX, Nonterminal, was not found in name map.)
(Residue 244: GLN, Nonterminal, was not found in name map.)
(Residue 245: THR, Nonterminal, was not found in name map.)
(Residue 246: PRO, Nonterminal, was not found in name map.)
(Residue 247: LYS, Nonterminal, was not found in name map.)
(Residue 248: GLY, Nonterminal, was not found in name map.)
(Residue 249: ALA, Nonterminal, was not found in name map.)
(Residue 250: ILE, Nonterminal, was not found in name map.)
(Residue 251: ASN, Nonterminal, was not found in name map.)
(Residue 252: THR, Nonterminal, was not found in name map.)
Mapped residue SER, term: Terminal/last, seq. number: 253 to: CSER.
(Residue 254: OME, Terminal/beginning, was not found in name map.)
(Residue 255: NAG, Nonterminal, was not found in name map.)
Unknown residue: NAG number: 255 type: Nonterminal
(Residue 256: GAL, Nonterminal, was not found in name map.)
Unknown residue: GAL number: 256 type: Nonterminal
(Residue 257: SIA, Terminal/last, was not found in name map.)
Unknown residue: SIA number: 257 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Joining NLYS - HIE
Joining HIE - ASN
Joining ASN - GLY
Joining GLY - LYS
Joining LYS - LEU
Joining LEU - CYX
Joining CYX - LYS
Joining LYS - LEU
Joining LEU - ARG
Joining ARG - GLY
Joining GLY - VAL
Joining VAL - ALA
Joining ALA - PRO
Joining PRO - LEU
Joining LEU - HIE
Joining HIE - LEU
Joining LEU - GLY
Joining GLY - LYS
Joining LYS - CYX
Joining CYX - ASN
Joining ASN - ILE
Joining ILE - ALA
Joining ALA - GLY
Joining GLY - TRP
Joining TRP - ILE
Joining ILE - LEU
Joining LEU - GLY
Joining GLY - ASN
Joining ASN - PRO
Joining PRO - GLU
Joining GLU - CYX
Joining CYX - GLU
Joining GLU - SER
Joining SER - LEU
Joining LEU - SER
Joining SER - THR
Joining THR - ALA
Joining ALA - SER
Joining SER - SER
Joining SER - TRP
Joining TRP - SER
Joining SER - TYR
Joining TYR - ILE
Joining ILE - VAL
Joining VAL - GLU
Joining GLU - THR
Joining THR - SER
Joining SER - SER
Joining SER - SER
Joining SER - ASP
Joining ASP - ASN
Joining ASN - GLY
Joining GLY - THR
Joining THR - CYX
Joining CYX - TYR
Joining TYR - PRO
Joining PRO - GLY
Joining GLY - ASP
Joining ASP - PHE
Joining PHE - ILE
Joining ILE - ASP
Joining ASP - TYR
Joining TYR - GLU
Joining GLU - GLU
Joining GLU - LEU
Joining LEU - ARG
Joining ARG - GLU
Joining GLU - GLN
Joining GLN - LEU
Joining LEU - SER
Joining SER - SER
Joining SER - VAL
Joining VAL - SER
Joining SER - SER
Joining SER - PHE
Joining PHE - GLU
Joining GLU - ARG
Joining ARG - PHE
Joining PHE - GLU
Joining GLU - ILE
Joining ILE - PHE
Joining PHE - PRO
Joining PRO - LYS
Joining LYS - THR
Joining THR - SER
Joining SER - SER
Joining SER - TRP
Joining TRP - PRO
Joining PRO - ASN
Joining ASN - HIE
Joining HIE - ASP
Joining ASP - SER
Joining SER - ASN
Joining ASN - LYS
Joining LYS - GLY
Joining GLY - VAL
Joining VAL - THR
Joining THR - ALA
Joining ALA - ALA
Joining ALA - CYX
Joining CYX - PRO
Joining PRO - HIE
Joining HIE - ALA
Joining ALA - GLY
Joining GLY - ALA
Joining ALA - LYS
Joining LYS - SER
Joining SER - PHE
Joining PHE - TYR
Joining TYR - LYS
Joining LYS - ASN
Joining ASN - LEU
Joining LEU - ILE
Joining ILE - TRP
Joining TRP - LEU
Joining LEU - VAL
Joining VAL - LYS
Joining LYS - LYS
Joining LYS - GLY
Joining GLY - ASN
Joining ASN - SER
Joining SER - TYR
Joining TYR - PRO
Joining PRO - LYS
Joining LYS - LEU
Joining LEU - SER
Joining SER - LYS
Joining LYS - SER
Joining SER - TYR
Joining TYR - ILE
Joining ILE - ASN
Joining ASN - ASP
Joining ASP - LYS
Joining LYS - GLY
Joining GLY - LYS
Joining LYS - GLU
Joining GLU - VAL
Joining VAL - LEU
Joining LEU - VAL
Joining VAL - LEU
Joining LEU - TRP
Joining TRP - GLY
Joining GLY - ILE
Joining ILE - HIE
Joining HIE - HIE
Joining HIE - PRO
Joining PRO - SER
Joining SER - THR
Joining THR - SER
Joining SER - ALA
Joining ALA - ASP
Joining ASP - GLN
Joining GLN - GLN
Joining GLN - SER
Joining SER - LEU
Joining LEU - TYR
Joining TYR - GLN
Joining GLN - ASN
Joining ASN - ALA
Joining ALA - ASP
Joining ASP - ALA
Joining ALA - TYR
Joining TYR - VAL
Joining VAL - PHE
Joining PHE - VAL
Joining VAL - GLY
Joining GLY - SER
Joining SER - SER
Joining SER - ARG
Joining ARG - TYR
Joining TYR - SER
Joining SER - LYS
Joining LYS - LYS
Joining LYS - PHE
Joining PHE - LYS
Joining LYS - PRO
Joining PRO - GLU
Joining GLU - ILE
Joining ILE - ALA
Joining ALA - ILE
Joining ILE - ARG
Joining ARG - PRO
Joining PRO - LYS
Joining LYS - VAL
Joining VAL - ARG
Joining ARG - GLY
Joining GLY - GLN
Joining GLN - GLU
Joining GLU - GLY
Joining GLY - ARG
Joining ARG - MET
Joining MET - ASN
Joining ASN - TYR
Joining TYR - TYR
Joining TYR - TRP
Joining TRP - THR
Joining THR - LEU
Joining LEU - VAL
Joining VAL - GLU
Joining GLU - PRO
Joining PRO - GLY
Joining GLY - ASP
Joining ASP - LYS
Joining LYS - ILE
Joining ILE - THR
Joining THR - PHE
Joining PHE - GLU
Joining GLU - ALA
Joining ALA - THR
Joining THR - GLY
Joining GLY - ASN
Joining ASN - LEU
Joining LEU - VAL
Joining VAL - VAL
Joining VAL - PRO
Joining PRO - ARG
Joining ARG - TYR
Joining TYR - ALA
Joining ALA - PHE
Joining PHE - ALA
Joining ALA - MET
Joining MET - GLU
Joining GLU - ARG
Joining ARG - ASN
Joining ASN - ALA
Joining ALA - GLY
Joining GLY - SER
Joining SER - GLY
Joining GLY - ILE
Joining ILE - ILE
Joining ILE - ILE
Joining ILE - SER
Joining SER - ASP
Joining ASP - THR
Joining THR - PRO
Joining PRO - VAL
Joining VAL - HIE
Joining HIE - ASP
Joining ASP - CYX
Joining CYX - ASN
Joining ASN - THR
Joining THR - THR
Joining THR - CYX
Joining CYX - GLN
Joining GLN - THR
Joining THR - PRO
Joining PRO - LYS
Joining LYS - GLY
Joining GLY - ALA
Joining ALA - ILE
Joining ILE - ASN
Joining ASN - THR
Joining THR - CSER
Created a new atom named: H12 within residue: .R<OME 255>
Creating new UNIT for residue: NAG sequence: 256
One sided connection. Residue: missing connect0 atom.
Created a new atom named: C1 within residue: .R<NAG 256>
Created a new atom named: H10 within residue: .R<NAG 256>
Created a new atom named: O5 within residue: .R<NAG 256>
Created a new atom named: C5 within residue: .R<NAG 256>
Created a new atom named: H5 within residue: .R<NAG 256>
Created a new atom named: C6 within residue: .R<NAG 256>
Created a new atom named: H61 within residue: .R<NAG 256>
Created a new atom named: H62 within residue: .R<NAG 256>
Created a new atom named: O6 within residue: .R<NAG 256>
Created a new atom named: H6O within residue: .R<NAG 256>
Created a new atom named: C2 within residue: .R<NAG 256>
Created a new atom named: H14 within residue: .R<NAG 256>
Created a new atom named: N2 within residue: .R<NAG 256>
Created a new atom named: H2N within residue: .R<NAG 256>
Created a new atom named: C2N within residue: .R<NAG 256>
Created a new atom named: O2N within residue: .R<NAG 256>
Created a new atom named: CME within residue: .R<NAG 256>
Created a new atom named: H1M within residue: .R<NAG 256>
Created a new atom named: H2M within residue: .R<NAG 256>
Created a new atom named: H3M within residue: .R<NAG 256>
Created a new atom named: C3 within residue: .R<NAG 256>
Created a new atom named: H13 within residue: .R<NAG 256>
Created a new atom named: O3 within residue: .R<NAG 256>
Created a new atom named: H3O within residue: .R<NAG 256>
Created a new atom named: C4 within residue: .R<NAG 256>
Created a new atom named: H4 within residue: .R<NAG 256>
Created a new atom named: O4 within residue: .R<NAG 256>
Creating new UNIT for residue: GAL sequence: 257
Starting new chain with
Created a new atom named: C10 within residue: .R<GAL 257>
Created a new atom named: H11 within residue: .R<GAL 257>
Created a new atom named: O10 within residue: .R<GAL 257>
Created a new atom named: C20 within residue: .R<GAL 257>
Created a new atom named: H16 within residue: .R<GAL 257>
Created a new atom named: O2 within residue: .R<GAL 257>
Created a new atom named: H2O within residue: .R<GAL 257>
Created a new atom named: C18 within residue: .R<GAL 257>
Created a new atom named: H15 within residue: .R<GAL 257>
Created a new atom named: O13 within residue: .R<GAL 257>
Created a new atom named: H23 within residue: .R<GAL 257>
Created a new atom named: C16 within residue: .R<GAL 257>
Created a new atom named: H21 within residue: .R<GAL 257>
Created a new atom named: O14 within residue: .R<GAL 257>
Created a new atom named: H4O within residue: .R<GAL 257>
Created a new atom named: C12 within residue: .R<GAL 257>
Created a new atom named: H17 within residue: .R<GAL 257>
Created a new atom named: C14 within residue: .R<GAL 257>
Created a new atom named: H19 within residue: .R<GAL 257>
Created a new atom named: H20 within residue: .R<GAL 257>
Created a new atom named: O11 within residue: .R<GAL 257>
Created a new atom named: C21 within residue: .R<GAL 257>
Creating new UNIT for residue: SIA sequence: 258
Starting new chain with
Created a new atom named: C11 within residue: .R<SIA 258>
Created a new atom named: O1A within residue: .R<SIA 258>
Created a new atom named: O1B within residue: .R<SIA 258>
Created a new atom named: C19 within residue: .R<SIA 258>
Created a new atom named: H3A within residue: .R<SIA 258>
Created a new atom named: H3E within residue: .R<SIA 258>
Created a new atom named: C17 within residue: .R<SIA 258>
Created a new atom named: H22 within residue: .R<SIA 258>
Created a new atom named: O15 within residue: .R<SIA 258>
Created a new atom named: H27 within residue: .R<SIA 258>
Created a new atom named: C13 within residue: .R<SIA 258>
Created a new atom named: H18 within residue: .R<SIA 258>
Created a new atom named: N5 within residue: .R<SIA 258>
Created a new atom named: H5N within residue: .R<SIA 258>
Created a new atom named: C5N within residue: .R<SIA 258>
Created a new atom named: O5N within residue: .R<SIA 258>
Created a new atom named: C22 within residue: .R<SIA 258>
Created a new atom named: H24 within residue: .R<SIA 258>
Created a new atom named: H25 within residue: .R<SIA 258>
Created a new atom named: H26 within residue: .R<SIA 258>
Created a new atom named: O12 within residue: .R<SIA 258>
Created a new atom named: C15 within residue: .R<SIA 258>
Created a new atom named: H6 within residue: .R<SIA 258>
Created a new atom named: C7 within residue: .R<SIA 258>
Created a new atom named: H7 within residue: .R<SIA 258>
Created a new atom named: O7 within residue: .R<SIA 258>
Created a new atom named: H7O within residue: .R<SIA 258>
Created a new atom named: C8 within residue: .R<SIA 258>
Created a new atom named: H8 within residue: .R<SIA 258>
Created a new atom named: O8 within residue: .R<SIA 258>
Created a new atom named: H8O within residue: .R<SIA 258>
Created a new atom named: C9 within residue: .R<SIA 258>
Created a new atom named: H9R within residue: .R<SIA 258>
Created a new atom named: H9S within residue: .R<SIA 258>
Created a new atom named: O9 within residue: .R<SIA 258>
Created a new atom named: H9O within residue: .R<SIA 258>
total atoms in file: 4003
Leap added 1 missing atom according to residue templates:
1 H / lone pairs
The file contained 86 atoms not in residue templates
> check COMPLEX
Checking 'COMPLEX'....
ERROR: The unperturbed charge of the unit: 4.806000 is not integral.
WARNING: The unperturbed charge of the unit: 4.806000 is not zero.
FATAL: Atom .R<OME 255>.A<H12 6> does not have a type.
FATAL: Atom .R<NAG 256>.A<C1 1> does not have a type.
FATAL: Atom .R<NAG 256>.A<H10 2> does not have a type.
FATAL: Atom .R<NAG 256>.A<O5 3> does not have a type.
FATAL: Atom .R<NAG 256>.A<C5 4> does not have a type.
FATAL: Atom .R<NAG 256>.A<H5 5> does not have a type.
FATAL: Atom .R<NAG 256>.A<C6 6> does not have a type.
FATAL: Atom .R<NAG 256>.A<H61 7> does not have a type.
FATAL: Atom .R<NAG 256>.A<H62 8> does not have a type.
FATAL: Atom .R<NAG 256>.A<O6 9> does not have a type.
FATAL: Atom .R<NAG 256>.A<H6O 10> does not have a type.
FATAL: Atom .R<NAG 256>.A<C2 11> does not have a type.
FATAL: Atom .R<NAG 256>.A<H14 12> does not have a type.
FATAL: Atom .R<NAG 256>.A<N2 13> does not have a type.
FATAL: Atom .R<NAG 256>.A<H2N 14> does not have a type.
FATAL: Atom .R<NAG 256>.A<C2N 15> does not have a type.
FATAL: Atom .R<NAG 256>.A<O2N 16> does not have a type.
FATAL: Atom .R<NAG 256>.A<CME 17> does not have a type.
FATAL: Atom .R<NAG 256>.A<H1M 18> does not have a type.
FATAL: Atom .R<NAG 256>.A<H2M 19> does not have a type.
FATAL: Atom .R<NAG 256>.A<H3M 20> does not have a type.
FATAL: Atom .R<NAG 256>.A<C3 21> does not have a type.
FATAL: Atom .R<NAG 256>.A<H13 22> does not have a type.
FATAL: Atom .R<NAG 256>.A<O3 23> does not have a type.
FATAL: Atom .R<NAG 256>.A<H3O 24> does not have a type.
FATAL: Atom .R<NAG 256>.A<C4 25> does not have a type.
FATAL: Atom .R<NAG 256>.A<H4 26> does not have a type.
FATAL: Atom .R<NAG 256>.A<O4 27> does not have a type.
FATAL: Atom .R<GAL 257>.A<C10 1> does not have a type.
FATAL: Atom .R<GAL 257>.A<H11 2> does not have a type.
FATAL: Atom .R<GAL 257>.A<O10 3> does not have a type.
FATAL: Atom .R<GAL 257>.A<C20 4> does not have a type.
FATAL: Atom .R<GAL 257>.A<H16 5> does not have a type.
FATAL: Atom .R<GAL 257>.A<O2 6> does not have a type.
FATAL: Atom .R<GAL 257>.A<H2O 7> does not have a type.
FATAL: Atom .R<GAL 257>.A<C18 8> does not have a type.
FATAL: Atom .R<GAL 257>.A<H15 9> does not have a type.
FATAL: Atom .R<GAL 257>.A<O13 10> does not have a type.
FATAL: Atom .R<GAL 257>.A<H23 11> does not have a type.
FATAL: Atom .R<GAL 257>.A<C16 12> does not have a type.
FATAL: Atom .R<GAL 257>.A<H21 13> does not have a type.
FATAL: Atom .R<GAL 257>.A<O14 14> does not have a type.
FATAL: Atom .R<GAL 257>.A<H4O 15> does not have a type.
FATAL: Atom .R<GAL 257>.A<C12 16> does not have a type.
FATAL: Atom .R<GAL 257>.A<H17 17> does not have a type.
FATAL: Atom .R<GAL 257>.A<C14 18> does not have a type.
FATAL: Atom .R<GAL 257>.A<H19 19> does not have a type.
FATAL: Atom .R<GAL 257>.A<H20 20> does not have a type.
FATAL: Atom .R<GAL 257>.A<O11 21> does not have a type.
FATAL: Atom .R<GAL 257>.A<C21 22> does not have a type.
FATAL: Atom .R<SIA 258>.A<C11 1> does not have a type.
FATAL: Atom .R<SIA 258>.A<O1A 2> does not have a type.
FATAL: Atom .R<SIA 258>.A<O1B 3> does not have a type.
FATAL: Atom .R<SIA 258>.A<C19 4> does not have a type.
FATAL: Atom .R<SIA 258>.A<H3A 5> does not have a type.
FATAL: Atom .R<SIA 258>.A<H3E 6> does not have a type.
FATAL: Atom .R<SIA 258>.A<C17 7> does not have a type.
FATAL: Atom .R<SIA 258>.A<H22 8> does not have a type.
FATAL: Atom .R<SIA 258>.A<O15 9> does not have a type.
FATAL: Atom .R<SIA 258>.A<H27 10> does not have a type.
FATAL: Atom .R<SIA 258>.A<C13 11> does not have a type.
FATAL: Atom .R<SIA 258>.A<H18 12> does not have a type.
FATAL: Atom .R<SIA 258>.A<N5 13> does not have a type.
FATAL: Atom .R<SIA 258>.A<H5N 14> does not have a type.
FATAL: Atom .R<SIA 258>.A<C5N 15> does not have a type.
FATAL: Atom .R<SIA 258>.A<O5N 16> does not have a type.
FATAL: Atom .R<SIA 258>.A<C22 17> does not have a type.
FATAL: Atom .R<SIA 258>.A<H24 18> does not have a type.
FATAL: Atom .R<SIA 258>.A<H25 19> does not have a type.
FATAL: Atom .R<SIA 258>.A<H26 20> does not have a type.
FATAL: Atom .R<SIA 258>.A<O12 21> does not have a type.
FATAL: Atom .R<SIA 258>.A<C15 22> does not have a type.
FATAL: Atom .R<SIA 258>.A<H6 23> does not have a type.
FATAL: Atom .R<SIA 258>.A<C7 24> does not have a type.
FATAL: Atom .R<SIA 258>.A<H7 25> does not have a type.
FATAL: Atom .R<SIA 258>.A<O7 26> does not have a type.
FATAL: Atom .R<SIA 258>.A<H7O 27> does not have a type.
FATAL: Atom .R<SIA 258>.A<C8 28> does not have a type.
FATAL: Atom .R<SIA 258>.A<H8 29> does not have a type.
FATAL: Atom .R<SIA 258>.A<O8 30> does not have a type.
FATAL: Atom .R<SIA 258>.A<H8O 31> does not have a type.
FATAL: Atom .R<SIA 258>.A<C9 32> does not have a type.
FATAL: Atom .R<SIA 258>.A<H9R 33> does not have a type.
FATAL: Atom .R<SIA 258>.A<H9S 34> does not have a type.
FATAL: Atom .R<SIA 258>.A<O9 35> does not have a type.
FATAL: Atom .R<SIA 258>.A<H9O 36> does not have a type.
Warning: Close contact of 1.949100 angstroms between .R<OME 255>.A<O 5> and
.R<NAG 256>.A<C1 1>
Warning: Close contact of 0.003510 angstroms between .R<OME 255>.A<H3 4> and
.R<OME 255>.A<H12 6>
Warning: Close contact of 1.211700 angstroms between .R<OME 255>.A<CH3 2>
and .R<OME 255>.A<H12 6>
Warning: Close contact of 1.190900 angstroms between .R<NAG 256>.A<C1 1> and
.R<NAG 256>.A<H10 2>
Warning: Close contact of 1.950900 angstroms between .R<NAG 256>.A<C1 1> and
.R<NAG 256>.A<O5 3>
Warning: Close contact of 1.868900 angstroms between .R<NAG 256>.A<O5 3> and
.R<NAG 256>.A<C5 4>
Warning: Close contact of 1.184300 angstroms between .R<NAG 256>.A<C5 4> and
.R<NAG 256>.A<H5 5>
Warning: Close contact of 1.196600 angstroms between .R<NAG 256>.A<C6 6> and
.R<NAG 256>.A<H61 7>
Warning: Close contact of 1.177700 angstroms between .R<NAG 256>.A<C6 6> and
.R<NAG 256>.A<H62 8>
Warning: Close contact of 2.181700 angstroms between .R<NAG 256>.A<C6 6> and
.R<NAG 256>.A<O6 9>
Warning: Close contact of 0.915800 angstroms between .R<NAG 256>.A<O6 9> and
.R<NAG 256>.A<H6O 10>
Warning: Close contact of 1.170900 angstroms between .R<NAG 256>.A<C2 11>
and .R<NAG 256>.A<H14 12>
Warning: Close contact of 2.040100 angstroms between .R<NAG 256>.A<C2 11>
and .R<NAG 256>.A<N2 13>
Warning: Close contact of 1.033400 angstroms between .R<NAG 256>.A<N2 13>
and .R<NAG 256>.A<H2N 14>
Warning: Close contact of 1.742400 angstroms between .R<NAG 256>.A<N2 13>
and .R<NAG 256>.A<C2N 15>
Warning: Close contact of 1.591200 angstroms between .R<NAG 256>.A<C2N 15>
and .R<NAG 256>.A<O2N 16>
Warning: Close contact of 2.239400 angstroms between .R<NAG 256>.A<C2N 15>
and .R<NAG 256>.A<CME 17>
Warning: Close contact of 1.185200 angstroms between .R<NAG 256>.A<CME 17>
and .R<NAG 256>.A<H1M 18>
Warning: Close contact of 1.200300 angstroms between .R<NAG 256>.A<CME 17>
and .R<NAG 256>.A<H2M 19>
Warning: Close contact of 1.191200 angstroms between .R<NAG 256>.A<CME 17>
and .R<NAG 256>.A<H3M 20>
Warning: Close contact of 1.192100 angstroms between .R<NAG 256>.A<C3 21>
and .R<NAG 256>.A<H13 22>
Warning: Close contact of 2.045900 angstroms between .R<NAG 256>.A<C3 21>
and .R<NAG 256>.A<O3 23>
Warning: Close contact of 0.931400 angstroms between .R<NAG 256>.A<O3 23>
and .R<NAG 256>.A<H3O 24>
Warning: Close contact of 1.190600 angstroms between .R<NAG 256>.A<C4 25>
and .R<NAG 256>.A<H4 26>
Warning: Close contact of 2.069700 angstroms between .R<NAG 256>.A<C4 25>
and .R<NAG 256>.A<O4 27>
Warning: Close contact of 2.093100 angstroms between .R<NAG 256>.A<O4 27>
and .R<GAL 257>.A<C10 1>
Warning: Close contact of 1.182500 angstroms between .R<GAL 257>.A<C10 1>
and .R<GAL 257>.A<H11 2>
Warning: Close contact of 2.045700 angstroms between .R<GAL 257>.A<C10 1>
and .R<GAL 257>.A<O10 3>
Warning: Close contact of 2.175000 angstroms between .R<GAL 257>.A<O10 3>
and .R<GAL 257>.A<C12 16>
Warning: Close contact of 1.180900 angstroms between .R<GAL 257>.A<C20 4>
and .R<GAL 257>.A<H16 5>
Warning: Close contact of 2.055300 angstroms between .R<GAL 257>.A<C20 4>
and .R<GAL 257>.A<O2 6>
Warning: Close contact of 2.221400 angstroms between .R<GAL 257>.A<C20 4>
and .R<GAL 257>.A<C18 8>
Warning: Close contact of 0.918200 angstroms between .R<GAL 257>.A<O2 6> and
.R<GAL 257>.A<H2O 7>
Warning: Close contact of 1.190700 angstroms between .R<GAL 257>.A<C18 8>
and .R<GAL 257>.A<H15 9>
Warning: Close contact of 2.015200 angstroms between .R<GAL 257>.A<C18 8>
and .R<GAL 257>.A<O13 10>
Warning: Close contact of 0.924900 angstroms between .R<GAL 257>.A<O13 10>
and .R<GAL 257>.A<H23 11>
Warning: Close contact of 1.184600 angstroms between .R<GAL 257>.A<C16 12>
and .R<GAL 257>.A<H21 13>
Warning: Close contact of 2.122100 angstroms between .R<GAL 257>.A<C16 12>
and .R<GAL 257>.A<O14 14>
Warning: Close contact of 0.935600 angstroms between .R<GAL 257>.A<O14 14>
and .R<GAL 257>.A<H4O 15>
Warning: Close contact of 1.175600 angstroms between .R<GAL 257>.A<C12 16>
and .R<GAL 257>.A<H17 17>
Warning: Close contact of 1.188600 angstroms between .R<GAL 257>.A<C14 18>
and .R<GAL 257>.A<H19 19>
Warning: Close contact of 1.187000 angstroms between .R<GAL 257>.A<C14 18>
and .R<GAL 257>.A<H20 20>
Warning: Close contact of 2.179500 angstroms between .R<GAL 257>.A<C14 18>
and .R<GAL 257>.A<O11 21>
Warning: Close contact of 2.152100 angstroms between .R<GAL 257>.A<O11 21>
and .R<GAL 257>.A<C21 22>
Warning: Close contact of 1.974500 angstroms between .R<GAL 257>.A<C21 22>
and .R<SIA 258>.A<O12 21>
Warning: Close contact of 1.632100 angstroms between .R<SIA 258>.A<C11 1>
and .R<SIA 258>.A<O1A 2>
Warning: Close contact of 1.530900 angstroms between .R<SIA 258>.A<C11 1>
and .R<SIA 258>.A<O1B 3>
Warning: Close contact of 1.189100 angstroms between .R<SIA 258>.A<C19 4>
and .R<SIA 258>.A<H3A 5>
Warning: Close contact of 1.181900 angstroms between .R<SIA 258>.A<C19 4>
and .R<SIA 258>.A<H3E 6>
Warning: Close contact of 1.183800 angstroms between .R<SIA 258>.A<C17 7>
and .R<SIA 258>.A<H22 8>
Warning: Close contact of 1.959300 angstroms between .R<SIA 258>.A<C17 7>
and .R<SIA 258>.A<O15 9>
Warning: Close contact of 0.922600 angstroms between .R<SIA 258>.A<O15 9>
and .R<SIA 258>.A<H27 10>
Warning: Close contact of 1.188900 angstroms between .R<SIA 258>.A<C13 11>
and .R<SIA 258>.A<H18 12>
Warning: Close contact of 2.213600 angstroms between .R<SIA 258>.A<C13 11>
and .R<SIA 258>.A<N5 13>
Warning: Close contact of 1.011000 angstroms between .R<SIA 258>.A<N5 13>
and .R<SIA 258>.A<H5N 14>
Warning: Close contact of 1.853800 angstroms between .R<SIA 258>.A<N5 13>
and .R<SIA 258>.A<C5N 15>
Warning: Close contact of 1.493400 angstroms between .R<SIA 258>.A<C5N 15>
and .R<SIA 258>.A<O5N 16>
Warning: Close contact of 1.193400 angstroms between .R<SIA 258>.A<C22 17>
and .R<SIA 258>.A<H24 18>
Warning: Close contact of 1.189400 angstroms between .R<SIA 258>.A<C22 17>
and .R<SIA 258>.A<H25 19>
Warning: Close contact of 1.194200 angstroms between .R<SIA 258>.A<C22 17>
and .R<SIA 258>.A<H26 20>
Warning: Close contact of 2.121400 angstroms between .R<SIA 258>.A<O12 21>
and .R<SIA 258>.A<C15 22>
Warning: Close contact of 1.185800 angstroms between .R<SIA 258>.A<C15 22>
and .R<SIA 258>.A<H6 23>
Warning: Close contact of 1.203000 angstroms between .R<SIA 258>.A<C7 24>
and .R<SIA 258>.A<H7 25>
Warning: Close contact of 2.043800 angstroms between .R<SIA 258>.A<C7 24>
and .R<SIA 258>.A<O7 26>
Warning: Close contact of 0.931300 angstroms between .R<SIA 258>.A<O7 26>
and .R<SIA 258>.A<H7O 27>
Warning: Close contact of 1.195400 angstroms between .R<SIA 258>.A<C8 28>
and .R<SIA 258>.A<H8 29>
Warning: Close contact of 2.067700 angstroms between .R<SIA 258>.A<C8 28>
and .R<SIA 258>.A<O8 30>
Warning: Close contact of 0.924200 angstroms between .R<SIA 258>.A<O8 30>
and .R<SIA 258>.A<H8O 31>
Warning: Close contact of 1.198600 angstroms between .R<SIA 258>.A<C9 32>
and .R<SIA 258>.A<H9R 33>
Warning: Close contact of 1.181700 angstroms between .R<SIA 258>.A<C9 32>
and .R<SIA 258>.A<H9S 34>
Warning: Close contact of 2.077400 angstroms between .R<SIA 258>.A<C9 32>
and .R<SIA 258>.A<O9 35>
Warning: Close contact of 0.922900 angstroms between .R<SIA 258>.A<O9 35>
and .R<SIA 258>.A<H9O 36>
Checking parameters for unit 'COMPLEX'.
Checking for bond parameters.
Checking for angle parameters.
check: Errors: 87 Warnings: 73
Checking Unit.
ERROR: The unperturbed charge of the unit: 4.806000 is not integral.
WARNING: The unperturbed charge of the unit: 4.806000 is not zero.
FATAL: Atom .R<OME 255>.A<H12 6> does not have a type.
FATAL: Atom .R<NAG 256>.A<C1 1> does not have a type.
FATAL: Atom .R<NAG 256>.A<H10 2> does not have a type.
FATAL: Atom .R<NAG 256>.A<O5 3> does not have a type.
FATAL: Atom .R<NAG 256>.A<C5 4> does not have a type.
FATAL: Atom .R<NAG 256>.A<H5 5> does not have a type.
FATAL: Atom .R<NAG 256>.A<C6 6> does not have a type.
FATAL: Atom .R<NAG 256>.A<H61 7> does not have a type.
FATAL: Atom .R<NAG 256>.A<H62 8> does not have a type.
FATAL: Atom .R<NAG 256>.A<O6 9> does not have a type.
FATAL: Atom .R<NAG 256>.A<H6O 10> does not have a type.
FATAL: Atom .R<NAG 256>.A<C2 11> does not have a type.
FATAL: Atom .R<NAG 256>.A<H14 12> does not have a type.
FATAL: Atom .R<NAG 256>.A<N2 13> does not have a type.
FATAL: Atom .R<NAG 256>.A<H2N 14> does not have a type.
FATAL: Atom .R<NAG 256>.A<C2N 15> does not have a type.
FATAL: Atom .R<NAG 256>.A<O2N 16> does not have a type.
FATAL: Atom .R<NAG 256>.A<CME 17> does not have a type.
FATAL: Atom .R<NAG 256>.A<H1M 18> does not have a type.
FATAL: Atom .R<NAG 256>.A<H2M 19> does not have a type.
FATAL: Atom .R<NAG 256>.A<H3M 20> does not have a type.
FATAL: Atom .R<NAG 256>.A<C3 21> does not have a type.
FATAL: Atom .R<NAG 256>.A<H13 22> does not have a type.
FATAL: Atom .R<NAG 256>.A<O3 23> does not have a type.
FATAL: Atom .R<NAG 256>.A<H3O 24> does not have a type.
FATAL: Atom .R<NAG 256>.A<C4 25> does not have a type.
FATAL: Atom .R<NAG 256>.A<H4 26> does not have a type.
FATAL: Atom .R<NAG 256>.A<O4 27> does not have a type.
FATAL: Atom .R<GAL 257>.A<C10 1> does not have a type.
FATAL: Atom .R<GAL 257>.A<H11 2> does not have a type.
FATAL: Atom .R<GAL 257>.A<O10 3> does not have a type.
FATAL: Atom .R<GAL 257>.A<C20 4> does not have a type.
FATAL: Atom .R<GAL 257>.A<H16 5> does not have a type.
FATAL: Atom .R<GAL 257>.A<O2 6> does not have a type.
FATAL: Atom .R<GAL 257>.A<H2O 7> does not have a type.
FATAL: Atom .R<GAL 257>.A<C18 8> does not have a type.
FATAL: Atom .R<GAL 257>.A<H15 9> does not have a type.
FATAL: Atom .R<GAL 257>.A<O13 10> does not have a type.
FATAL: Atom .R<GAL 257>.A<H23 11> does not have a type.
FATAL: Atom .R<GAL 257>.A<C16 12> does not have a type.
FATAL: Atom .R<GAL 257>.A<H21 13> does not have a type.
FATAL: Atom .R<GAL 257>.A<O14 14> does not have a type.
FATAL: Atom .R<GAL 257>.A<H4O 15> does not have a type.
FATAL: Atom .R<GAL 257>.A<C12 16> does not have a type.
FATAL: Atom .R<GAL 257>.A<H17 17> does not have a type.
FATAL: Atom .R<GAL 257>.A<C14 18> does not have a type.
FATAL: Atom .R<GAL 257>.A<H19 19> does not have a type.
FATAL: Atom .R<GAL 257>.A<H20 20> does not have a type.
FATAL: Atom .R<GAL 257>.A<O11 21> does not have a type.
FATAL: Atom .R<GAL 257>.A<C21 22> does not have a type.
FATAL: Atom .R<SIA 258>.A<C11 1> does not have a type.
FATAL: Atom .R<SIA 258>.A<O1A 2> does not have a type.
FATAL: Atom .R<SIA 258>.A<O1B 3> does not have a type.
FATAL: Atom .R<SIA 258>.A<C19 4> does not have a type.
FATAL: Atom .R<SIA 258>.A<H3A 5> does not have a type.
FATAL: Atom .R<SIA 258>.A<H3E 6> does not have a type.
FATAL: Atom .R<SIA 258>.A<C17 7> does not have a type.
FATAL: Atom .R<SIA 258>.A<H22 8> does not have a type.
FATAL: Atom .R<SIA 258>.A<O15 9> does not have a type.
FATAL: Atom .R<SIA 258>.A<H27 10> does not have a type.
FATAL: Atom .R<SIA 258>.A<C13 11> does not have a type.
FATAL: Atom .R<SIA 258>.A<H18 12> does not have a type.
FATAL: Atom .R<SIA 258>.A<N5 13> does not have a type.
FATAL: Atom .R<SIA 258>.A<H5N 14> does not have a type.
FATAL: Atom .R<SIA 258>.A<C5N 15> does not have a type.
FATAL: Atom .R<SIA 258>.A<O5N 16> does not have a type.
FATAL: Atom .R<SIA 258>.A<C22 17> does not have a type.
FATAL: Atom .R<SIA 258>.A<H24 18> does not have a type.
FATAL: Atom .R<SIA 258>.A<H25 19> does not have a type.
FATAL: Atom .R<SIA 258>.A<H26 20> does not have a type.
FATAL: Atom .R<SIA 258>.A<O12 21> does not have a type.
FATAL: Atom .R<SIA 258>.A<C15 22> does not have a type.
FATAL: Atom .R<SIA 258>.A<H6 23> does not have a type.
FATAL: Atom .R<SIA 258>.A<C7 24> does not have a type.
FATAL: Atom .R<SIA 258>.A<H7 25> does not have a type.
FATAL: Atom .R<SIA 258>.A<O7 26> does not have a type.
FATAL: Atom .R<SIA 258>.A<H7O 27> does not have a type.
FATAL: Atom .R<SIA 258>.A<C8 28> does not have a type.
FATAL: Atom .R<SIA 258>.A<H8 29> does not have a type.
FATAL: Atom .R<SIA 258>.A<O8 30> does not have a type.
FATAL: Atom .R<SIA 258>.A<H8O 31> does not have a type.
FATAL: Atom .R<SIA 258>.A<C9 32> does not have a type.
FATAL: Atom .R<SIA 258>.A<H9R 33> does not have a type.
FATAL: Atom .R<SIA 258>.A<H9S 34> does not have a type.
FATAL: Atom .R<SIA 258>.A<O9 35> does not have a type.
FATAL: Atom .R<SIA 258>.A<H9O 36> does not have a type.
Failed to generate parameters
Parameter file was not saved.
Quit
--
Chris Whittleston
Department of Chemistry
University of Cambridge
Lensfield Road, Cambridge, CB2 1EW
Email: csw34.cam.ac.uk
Tel: +44 (0)1223 336423
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Received on Mon Jul 05 2010 - 09:00:03 PDT
