AMBER Archive (2009)

Subject: [AMBER] fatal "does not have a type" error in tleap for a protein-ligand complex

From: Jeff Yeo (weekiang_at_live.com)
Date: Wed Sep 23 2009 - 18:24:51 CDT

Hi there,

Here is the way I do it:
1) Use a docking package to create the following file:
i) complex.pdb file
 
This is the portion of the (of complex.pdb) file pertaining to the ligand:
TER 2203 ILE 277
HETATM 2204 C4 B49 A9000 42.046 7.076 27.957 1.00 17.32 C
HETATM 2205 H41 B49 A9000 41.704 8.017 28.387 1.00182327 H
HETATM 2206 H42 B49 A9000 42.769 7.280 27.167 1.00182327 H
HETATM 2207 H43 B49 A9000 42.516 6.472 28.733 1.00182327 H
HETATM 2208 C5 B49 A9000 40.418 -1.442 23.452 1.00 15.43 C
HETATM 2209 H5 B49 A9000 40.417 -2.415 22.983 1.00182328 H
HETATM 2210 C6 B49 A9000 41.645 -0.871 23.890 1.00 14.10 C
HETATM 2211 H6 B49 A9000 42.582 -1.391 23.761 1.00182328 H
HETATM 2212 C7 B49 A9000 39.147 0.542 24.241 1.00 15.14 C
HETATM 2213 H7 B49 A9000 38.213 1.068 24.370 1.00182328 H
HETATM 2214 C13 B49 A9000 38.907 5.504 26.646 1.00 17.58 C
HETATM 2215 C15 B49 A9000 39.190 -0.738 23.629 1.00 15.55 C
HETATM 2216 C17 B49 A9000 40.377 1.110 24.679 1.00 14.45 C
HETATM 2217 C20 B49 A9000 40.749 2.384 25.348 1.00 13.45 C
HETATM 2218 C21 B49 A9000 42.252 2.345 25.530 1.00 13.66 C
HETATM 2219 C22 B49 A9000 38.849 7.831 27.841 1.00 21.63 C
HETATM 2220 C3 B49 A9000 37.446 5.357 26.341 1.00 18.30 C
HETATM 2221 H31 B49 A9000 37.275 4.412 25.826 1.00178473 H
HETATM 2222 H32 B49 A9000 37.123 6.181 25.705 1.00178473 H
HETATM 2223 H33 B49 A9000 36.877 5.370 27.271 1.00178473 H
HETATM 2224 C12 B49 A9000 39.819 3.309 25.678 1.00 15.97 C
HETATM 2225 H12 B49 A9000 38.814 3.036 25.392 1.00178473 H
HETATM 2226 C14 B49 A9000 40.885 6.338 27.389 1.00 17.03 C
HETATM 2227 C16 B49 A9000 41.593 0.395 24.495 1.00 12.00 C
HETATM 2228 C18 B49 A9000 39.909 4.581 26.333 1.00 15.83 C
HETATM 2229 C19 B49 A9000 39.528 6.626 27.324 1.00 17.94 C
HETATM 2230 N23 B49 A9000 41.087 5.117 26.792 1.00 14.09 N
HETATM 2231 H23 B49 A9000 41.989 4.670 26.701 1.00178475 H
HETATM 2232 N24 B49 A9000 42.668 1.127 24.993 1.00 11.43 N
HETATM 2233 H24 B49 A9000 43.628 0.814 24.969 1.00178475 H
HETATM 2234 N25 B49 A9000 38.003 8.464 26.948 1.00 24.57 N
HETATM 2235 H251 B49 A9000 37.505 9.297 27.227 1.00178476 H
HETATM 2236 H252 B49 A9000 37.882 8.091 26.016 1.00178476 H
HETATM 2237 O27 B49 A9000 42.955 3.193 26.039 1.00 15.23 O
HETATM 2238 O28 B49 A9000 39.041 8.232 28.993 1.00 26.27 O
HETATM 2239 F29 B49 A9000 38.049 -1.302 23.202 1.00 17.21 F

Next, I proceeded to 'clean up' the above section by removing the HEADER, REMARK and CONNECT sections. Thereafter I manually re-numbered the atom numbers and changed HETATM to ATOM. I also changed the name of the residue to SUN and the residue number to 1. Columns 9 and 10 were also deleted. Lastly, I saved this changes and replaced the complex.pdb file.
 
I extracted the ligand portion and saved it as myligand.pdb.
 
This is the full contents of myligand.pdb file:
ATOM 2203 C1 SUN 1 42.046 7.076 27.957
ATOM 2204 H1 SUN 1 41.704 8.017 28.387
ATOM 2205 H2 SUN 1 42.769 7.280 27.167
ATOM 2206 H3 SUN 1 42.516 6.472 28.733
ATOM 2207 C2 SUN 1 40.418 -1.442 23.452
ATOM 2208 H4 SUN 1 40.417 -2.415 22.983
ATOM 2209 C3 SUN 1 41.645 -0.871 23.890
ATOM 2210 H5 SUN 1 42.582 -1.391 23.761
ATOM 2211 C4 SUN 1 39.147 0.542 24.241
ATOM 2212 H6 SUN 1 38.213 1.068 24.370
ATOM 2213 C5 SUN 1 38.907 5.504 26.646
ATOM 2214 C6 SUN 1 39.190 -0.738 23.629
ATOM 2215 C7 SUN 1 40.377 1.110 24.679
ATOM 2216 C8 SUN 1 40.749 2.384 25.348
ATOM 2217 C9 SUN 1 42.252 2.345 25.530
ATOM 2218 C10 SUN 1 38.849 7.831 27.841
ATOM 2219 C11 SUN 1 37.446 5.357 26.341
ATOM 2220 H7 SUN 1 37.275 4.412 25.826
ATOM 2221 H8 SUN 1 37.123 6.181 25.705
ATOM 2222 H9 SUN 1 36.877 5.370 27.271
ATOM 2223 C12 SUN 1 39.819 3.309 25.678
ATOM 2224 H10 SUN 1 38.814 3.036 25.392
ATOM 2225 C13 SUN 1 40.885 6.338 27.389
ATOM 2226 C14 SUN 1 41.593 0.395 24.495
ATOM 2227 C15 SUN 1 39.909 4.581 26.333
ATOM 2228 C16 SUN 1 39.528 6.626 27.324
ATOM 2229 N1 SUN 1 41.087 5.117 26.792
ATOM 2230 H2 SUN 1 41.989 4.670 26.701
ATOM 2231 N3 SUN 1 42.668 1.127 24.993
ATOM 2232 H11 SUN 1 43.628 0.814 24.969
ATOM 2233 N25 SUN 1 38.003 8.464 26.948
ATOM 2234 H12 SUN 1 37.505 9.297 27.227
ATOM 2235 H13 SUN 1 37.882 8.091 26.016
ATOM 2236 O1 SUN 1 42.955 3.193 26.039
ATOM 2237 O2 SUN 1 39.041 8.232 28.993
ATOM 2238 F1 SUN 1 38.049 -1.302 23.202
TER
END

 
2) Executed the command:
$AMBERHOME/exe/antechamber -i myligand.pdb -fi pdb -o myligand.com -fo gcrt
 
This is the full contents of myligand.com file:
--Link1--
%chk=SUN
#HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2) iop(6/42=6) opt
remark line goes here
0 1
    C 42.0460 7.0760 27.9570
    H 41.7040 8.0170 28.3870
    H 42.7690 7.2800 27.1670
    H 42.5160 6.4720 28.7330
    C 40.4180 -1.4420 23.4520
    H 40.4170 -2.4150 22.9830
    C 41.6450 -0.8710 23.8900
    H 42.5820 -1.3910 23.7610
    C 39.1470 0.5420 24.2410
    H 38.2130 1.0680 24.3700
    C 38.9070 5.5040 26.6460
    C 39.1900 -0.7380 23.6290
    C 40.3770 1.1100 24.6790
    C 40.7490 2.3840 25.3480
    C 42.2520 2.3450 25.5300
    C 38.8490 7.8310 27.8410
    C 37.4460 5.3570 26.3410
    H 37.2750 4.4120 25.8260
    H 37.1230 6.1810 25.7050
    H 36.8770 5.3700 27.2710
    C 39.8190 3.3090 25.6780
    H 38.8140 3.0360 25.3920
    C 40.8850 6.3380 27.3890
    C 41.5930 0.3950 24.4950
    C 39.9090 4.5810 26.3330
    C 39.5280 6.6260 27.3240
    N 41.0870 5.1170 26.7920
    H 41.9890 4.6700 26.7010
    N 42.6680 1.1270 24.9930
    H 43.6280 0.8140 24.9690
    N 38.0030 8.4640 26.9480
    H 37.5050 9.2970 27.2270
    H 37.8820 8.0910 26.0160
    O 42.9550 3.1930 26.0390
    O 39.0410 8.2320 28.9930
    F 38.0490 -1.3020 23.2020

3) Started Gaussian 03. File –> Open –> myligand.com
Click the “Run” button. Wait patiently.

4) Convergence is achieved, i.e. wait is finally over.

5) Gaussian output is in myligand.out.

6) Next, run:
$AMBERHOME/exe/antechamber -i myligand.out -fi gout -o myligand.prepi -fo prepi -c resp -s 2
 
This is the full contents of myligand.prepi (I changed the default MOL to SUN):
    0 0 2
This is a remark line
molecule.res
SUN 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 C1 c3 M 3 2 1 1.540 111.208 180.000 -0.393972
   5 H1 hc E 4 3 2 1.082 45.365 -93.873 0.133217
   6 H2 hc E 4 3 2 1.084 124.641 -10.730 0.133217
   7 H3 hc E 4 3 2 1.082 61.644 83.912 0.133217
   8 C13 cd M 4 3 2 1.497 124.412 -179.814 0.340664
   9 N1 na S 8 4 3 1.327 121.173 179.584 -0.386807
  10 H11 hn E 9 8 4 1.003 126.645 -0.853 0.423017
  11 C16 cc M 8 4 3 1.392 130.851 -0.564 -0.475723
  12 C10 c B 11 8 4 1.477 121.822 -0.115 0.922856
  13 N3 n B 12 11 8 1.368 117.412 163.638 -0.988747
  14 H13 hn E 13 12 11 0.997 114.107 -170.077 0.399465
  15 H14 hn E 13 12 11 0.993 119.619 -27.349 0.399465
  16 O2 o E 12 11 8 1.204 121.960 -16.985 -0.631911
  17 C5 cc M 11 8 4 1.421 107.212 -178.985 0.215167
  18 C11 c3 3 17 11 8 1.505 127.323 177.868 -0.320982
  19 H7 hc E 18 17 11 1.082 111.767 -159.395 0.100506
  20 H8 hc E 18 17 11 1.089 111.590 80.756 0.100506
  21 H9 hc E 18 17 11 1.081 110.847 -39.447 0.100506
  22 C15 cd M 17 11 8 1.382 106.596 -0.609 -0.087141
  23 C12 cf M 22 17 11 1.431 127.668 -179.745 -0.074965
  24 H10 ha E 23 22 17 1.074 112.531 -0.562 0.185371
  25 C8 cc M 23 22 17 1.349 133.039 179.213 -0.155598
  26 C7 ca M 25 23 22 1.471 125.531 -179.901 -0.056866
  27 C4 ca M 26 25 23 1.381 132.941 -0.051 -0.302321
  28 H6 ha E 27 26 25 1.074 122.936 -0.125 0.189355
  29 C6 ca M 27 26 25 1.383 117.824 179.988 0.355028
  30 F1 f E 29 27 26 1.334 118.290 179.942 -0.222988
  31 C2 ca M 29 27 26 1.376 122.881 -0.033 -0.292095
  32 H4 ha E 31 29 27 1.074 119.361 -179.975 0.196348
  33 C3 ca M 31 29 27 1.393 119.370 -0.001 -0.278497
  34 H5 ha E 33 31 29 1.075 120.349 -179.951 0.198252
  35 C14 ca M 33 31 29 1.374 118.147 0.014 0.294712
  36 N2 n M 35 33 31 1.396 129.389 -179.977 -0.676016
  37 H12 hn E 36 35 33 0.994 126.050 -0.239 0.404785
  38 C9 c M 36 35 33 1.362 112.379 -179.979 0.786459
  39 O1 o M 38 36 35 1.209 123.731 179.921 -0.667483

LOOP
  C15 N1
   C9 C8
  C14 C7
IMPROPER
   C1 C16 C13 N1
  C15 C13 N1 H11
  C10 C5 C16 C13
  C16 N3 C10 O2
  C10 H13 N3 H14
  C11 C16 C5 C15
   C5 C12 C15 N1
   C8 C15 C12 H10
   C9 C7 C8 C12
   C4 C14 C7 C8
   C7 C6 C4 H6
   C4 C2 C6 F1
   C6 C3 C2 H4
   C2 C14 C3 H5
   C7 C3 C14 N2
   C9 C14 N2 H12
   C8 N2 C9 O1
DONE
STOP

7) Test if all the parameters required are available.
$AMBERHOME/exe/parmchk -i myligand.prepi -f prepi -o myligand.frcmod
 
This is the full contents of myligand.frcmod file:
remark goes here
MASS
BOND
cd-cf 562.40 1.338 same as ce-cf
ANGLE
na-cd-cf 70.300 124.550 same as c2-c2-n3
cc-cd-cf 69.100 117.020 same as c2-cd-cc
cd-cf-ha 50.600 116.110 same as ce-cf-ha
cd-cf-cc 69.800 121.810 same as c2-c2-c2
cf-cc-ca 64.400 128.220 same as c2-cc-ca
cf-cc-c 64.300 126.410 same as c -ce-cf
DIHE
na-cd-cf-ha 1 6.650 180.000 2.000 same as X -ce-cf-X
na-cd-cf-cc 1 6.650 180.000 2.000 same as X -ce-cf-X
cc-cd-cf-ha 1 6.650 180.000 2.000 same as X -ce-cf-X
cc-cd-cf-cc 1 6.650 180.000 2.000 same as X -ce-cf-X
cd-cf-cc-ca 1 6.650 180.000 2.000 same as X -ce-cf-X
cd-cf-cc-c 1 6.650 180.000 2.000 same as X -ce-cf-X
cf-cc-ca-ca 1 2.550 180.000 2.000 same as X -c2-ca-X
ha-cf-cc-ca 1 6.650 180.000 2.000 same as X -ce-cf-X
ha-cf-cc-c 1 6.650 180.000 2.000 same as X -ce-cf-X
ca-ca-cc-c 1 2.550 180.000 2.000 same as X -c2-ca-X
IMPROPER
c3-cc-cd-na 1.1 180.0 2.0 Using default value
cd-cd-na-hn 1.1 180.0 2.0 General improper torsional angle (2 general atom types)
c -cc-cc-cd 1.1 180.0 2.0 Using default value
cc-n -c -o 10.5 180.0 2.0 General improper torsional angle (2 general atom types)
c -hn-n -hn 1.1 180.0 2.0 General improper torsional angle (2 general atom types)
c3-cc-cc-cd 1.1 180.0 2.0 Using default value
cc-cf-cd-na 1.1 180.0 2.0 Using default value
cc-cd-cf-ha 1.1 180.0 2.0 Using default value
c -ca-cc-cf 1.1 180.0 2.0 Using default value
ca-ca-ca-cc 1.1 180.0 2.0 Using default value
ca-ca-ca-ha 1.1 180.0 2.0 General improper torsional angle (2 general atom types)
ca-ca-ca-n 1.1 180.0 2.0 Using default value
c -ca-n -hn 1.1 180.0 2.0 General improper torsional angle (2 general atom types)
NONBON

8) Run tleap:
$AMBERHOME/exe/tleap
source leaprc.gaff
loadAmberPrep myligand.prepi
list
loadamberparams myligand.frcmod
check MOL
source leaprc.ff99SB
complex = loadpdb complex.pdb
check complex

The "check MOL" command proceeded without errors or warnings (Unit is OK). However, the "loadpdb" command gave me the following messages:
Loading PDB file: ./complex.pdb
-- residue 278: duplicate [ H2] atoms (total 2)
   Warning: Atom names in each residue should be unique.
     (Same-name atoms are handled by using the first
      occurrence and by ignoring the rest.
      Frequently duplicate atom names stem from alternate
      conformations in the PDB file.)
Created a new atom named: N25 within residue: .R<SUN 278>
  Added missing heavy atom: .R<SUN 278>.A<N2 33>
  total atoms in file: 2238
  Leap added 2201 missing atoms according to residue templates:
       1 Heavy
       2200 H / lone pairs
  The file contained 1 atoms not in residue templates

> check complex
Checking 'complex'....
WARNING: There is a bond of 9.857494 angstroms between:
------- .R<SUN 278>.A<N2 33> and .R<SUN 278>.A<H12 34>
WARNING: There is a bond of 8.511734 angstroms between:
------- .R<SUN 278>.A<N3 10> and .R<SUN 278>.A<H13 11>
WARNING: There is a bond of 8.224323 angstroms between:
------- .R<SUN 278>.A<C10 9> and .R<SUN 278>.A<N3 10>
WARNING: There is a bond of 5.319381 angstroms between:
------- .R<SUN 278>.A<N1 6> and .R<SUN 278>.A<H11 7>
WARNING: The unperturbed charge of the unit: -2.999999 is not zero.
FATAL: Atom .R<SUN 278>.A<N25 37> does not have a type.
*This is following by 65 close contact warnings that are not important at the moment.*
Checking parameters for unit 'complex'.
Checking for bond parameters.
Checking for angle parameters.
check: Errors: 1 Warnings: 65

Here are my queries:
1) May I know what caused the fatal "does not have a type" error?
2) Why is there a "mssing heavy atom"?
3) What are the possible remedies or solutions?
 
(I am aware that I should AddIons to neutralize the negative charge but I believe that is not causing the error.)
 
Thank you.
 
Sincerely,
Jeff Yeo
                                                
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