Hi Amber community,
I get this error when running tleap:
/opt/anaconda3/envs/AmberTools2023/bin/teLeap: Error!
Could not find bond parameter for atom types: C - NT
for atom C at position 19.936000, 29.132000, -46.146000
and atom N at position 18.802000, 28.748000, -46.764000.
I looked into the positions in my pdb file
ATOM 3916 C LYS A 255 19.936 29.132 -46.146 1.00 14.29 C
HETATM 3936 N MHS A 256 18.802 28.748 -46.764 1.00 13.66 N
This is between the N termini of my modified amino acid MHS and C termini of Lysine [I have checked the bond length and is about 1.3A which sounds reasonable and there definitely is a bond]
In my frcmod file, there is no C-NT which is what the error is telling me but there is CT-NT (which is what i believe should represent the bond above and not C-NT)
BOND
H -NT 434.00 1.010
CT-NT 367.00 1.471
CT-CT 310.00 1.526
CT-H1 340.00 1.090
C -CT 317.00 1.522
CC-CT 317.00 1.504
CT-HC 340.00 1.090
CC-N* 448.00 1.365 same as CM-N*, penalty score= 0.2
CC-CV 512.00 1.375
CR-N* 448.00 1.365 same as CM-N*, penalty score= 0.1
CT-N* 337.00 1.475
CR-NB 488.00 1.335
CR-H5 367.00 1.080
CV-NB 410.00 1.394
CV-H4 367.00 1.080
C -O 570.00 1.229
Anyone has suggestions on how i can fix this? I believe the definition of the bond should be NT-CT and not C - NT, not sure how i can "inform" the tleap
Additionally, this seems to be occurring for all my N termini of other modified amino acids (with the C-termini) present in the system so im probably doing something wrong in my treatment of N termini potentially. (where it should read NT-CT its reading C-NT and throwing an error). Is it potentially the protonation state of the N?
Any help would be appreciated. Thanks in advance
Additional details:
Ac file:
CHARGE 0.00 ( 0 )
Formula: H11 C7 N3 O2
ATOM 1 N MHS 1 -1.464 0.955 -1.050 -0.899800 NT
ATOM 2 CA MHS 1 -0.106 0.415 -1.204 0.132500 CT
ATOM 3 C MHS 1 0.115 0.018 -2.641 0.635100 C
ATOM 4 O MHS 1 -0.815 -0.351 -3.316 -0.541000 O
ATOM 5 CB MHS 1 0.059 -0.811 -0.305 -0.043100 CT
ATOM 6 CG MHS 1 -0.162 -0.414 1.131 -0.232900 CC
ATOM 7 ND1 MHS 1 0.790 0.013 2.016 -0.197900 N*
ATOM 8 CD2 MHS 1 -1.334 -0.420 1.794 0.302200 CV
ATOM 9 CE1 MHS 1 0.165 0.262 3.187 0.395400 CR
ATOM 10 NE2 MHS 1 -1.105 0.000 3.046 -0.663000 NB
ATOM 11 CM MHS 1 2.220 0.176 1.742 0.018600 CT
ATOM 12 OXT MHS 1 1.347 0.076 -3.171 -0.606100 OH
ATOM 13 H MHS 1 -1.604 1.109 -0.062 0.370800 H
ATOM 14 H2 MHS 1 -2.100 0.221 -1.322 0.370800 H
ATOM 15 HA MHS 1 0.621 1.175 -0.921 0.088700 H1
ATOM 16 HB2 MHS 1 1.067 -1.211 -0.420 0.072200 HC
ATOM 17 HB3 MHS 1 -0.668 -1.571 -0.589 0.072200 HC
ATOM 18 HD2 MHS 1 -2.292 -0.710 1.387 0.044100 H4
ATOM 19 HE1 MHS 1 0.638 0.619 4.090 0.063100 H5
ATOM 20 HM1 MHS 1 2.742 -0.752 1.970 0.057700 H1
ATOM 21 HM2 MHS 1 2.363 0.425 0.691 0.057700 H1
ATOM 22 HM3 MHS 1 2.620 0.978 2.363 0.057700 H1
ATOM 23 HXT MHS 1 1.489 -0.178 -4.093 0.448000 HO
BOND 1 1 2 1 N CA
BOND 2 1 13 1 N H
BOND 3 1 14 1 N H2
BOND 4 2 3 1 CA C
BOND 5 2 5 1 CA CB
BOND 6 2 15 1 CA HA
BOND 7 3 4 2 C O
BOND 8 3 12 1 C OXT
BOND 9 5 6 1 CB CG
BOND 10 5 16 1 CB HB2
BOND 11 5 17 1 CB HB3
BOND 12 6 7 7 CG ND1
BOND 13 6 8 8 CG CD2
BOND 14 7 9 7 ND1 CE1
BOND 15 7 11 1 ND1 CM
BOND 16 8 10 7 CD2 NE2
BOND 17 8 18 1 CD2 HD2
BOND 18 9 10 8 CE1 NE2
BOND 19 9 19 1 CE1 HE1
BOND 20 11 20 1 CM HM1
BOND 21 11 21 1 CM HM2
BOND 22 11 22 1 CM HM3
BOND 23 12 23 1 OXT HXT
Prepin file:
0 0 2
This is a remark line
molecule.res
MHS 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 1.523 111.21 .0 .00000
4 N NT M 3 2 1 1.540 111.208 -180.000 -0.861648
5 H2 H E 4 3 2 1.009 50.906 20.333 0.386522
6 CA CT M 4 3 2 1.470 157.535 15.918 0.138118
7 CB CT 3 6 4 3 1.529 109.433 -56.372 -0.041273
8 CG CC S 7 6 4 1.506 109.472 -60.095 -0.223025
9 ND1 N* B 8 7 6 1.368 126.647 -90.467 -0.189509
10 CE1 CR B 9 8 7 1.351 107.241 -179.991 0.412165
11 NE2 NB S 10 9 8 1.304 108.652 0.283 -0.634888
12 CD2 CV S 11 10 9 1.340 109.286 -0.041 0.315013
13 HD2 H4 E 12 11 10 1.081 125.977 179.938 0.045970
14 HE1 H5 E 10 9 8 1.080 125.675 -179.699 0.065775
15 CM CT 3 9 8 7 1.465 126.363 0.285 0.019389
16 HM1 H1 E 15 9 8 1.089 109.507 -90.381 0.060147
17 HM2 H1 E 15 9 8 1.090 109.508 29.702 0.060147
18 HM3 H1 E 15 9 8 1.090 109.474 149.713 0.060147
19 HB2 HC E 7 6 4 1.091 109.378 179.998 0.075261
20 HB3 HC E 7 6 4 1.089 109.514 60.020 0.075261
21 HA H1 E 6 4 3 1.089 109.463 -176.443 0.092461
22 C C M 6 4 3 1.507 109.404 63.578 0.662029
23 O O E 22 6 4 1.207 120.052 -29.934 -0.518061
LOOP
CD2 CG
IMPROPER
CB CD2 CG ND1
CG CE1 ND1 CM
HE1 ND1 CE1 NE2
CG HD2 CD2 NE2
CA +M C O
DONE
STOP
Mainchain file:
HEAD_NAME N
TAIL_NAME C
MAIN_CHAIN CA
OMIT_NAME H
OMIT_NAME OXT
OMIT_NAME HXT
PRE_HEAD_TYPE C
POST_TAIL_TYPE N
CHARGE 0.0
Frcmod file:
Remark line goes here
MASS
NT 14.010 0.530
H 1.008 0.161
CT 12.010 0.878
CC 12.010 0.360
N* 14.010 0.530
CR 12.010 0.360
NB 14.010 0.530
CV 12.010 0.360
H4 1.008 0.167
H5 1.008 0.167
H1 1.008 0.135
HC 1.008 0.135
C 12.010 0.616
O 16.000 0.434
BOND
H -NT 434.00 1.010
CT-NT 367.00 1.471
CT-CT 310.00 1.526
CT-H1 340.00 1.090
C -CT 317.00 1.522
CC-CT 317.00 1.504
CT-HC 340.00 1.090
CC-N* 448.00 1.365 same as CM-N*, penalty score= 0.2
CC-CV 512.00 1.375
CR-N* 448.00 1.365 same as CM-N*, penalty score= 0.1
CT-N* 337.00 1.475
CR-NB 488.00 1.335
CR-H5 367.00 1.080
CV-NB 410.00 1.394
CV-H4 367.00 1.080
C -O 570.00 1.229
ANGLE
CT-CT-NT 80.000 111.200
H1-CT-NT 50.000 109.500
C -CT-NT 80.000 111.200 same as C -CT-N3, penalty score= 0.1
CT-NT-H 50.000 109.500
CC-CT-CT 63.000 113.100
CT-CT-HC 50.000 109.500
CT-C -O 80.000 120.400
CT-CT-H1 50.000 109.500
C -CT-CT 63.000 111.100
CT-CC-N* 65.490 120.910 same as c3-cc-nc, penalty score= 0.0
CT-CC-CV 70.000 120.000
CC-CT-HC 50.000 109.500
CC-N*-CR 70.000 105.400 same as CB-N*-CK, penalty score= 0.2
CC-N*-CT 70.000 125.800 same as CB-N*-CT, penalty score= 0.1
CC-CV-NB 70.000 120.000
CC-CV-H4 50.000 120.000
CV-CC-N* 67.340 121.270 same as cc-cc-nc, penalty score= 0.0
N*-CR-NB 72.320 124.410 same as nc-cc-nc, penalty score= 0.0
H5-CR-N* 48.550 120.600 same as h5-cc-nc, penalty score= 0.0
H1-CT-N* 50.000 109.500
CR-N*-CT 70.000 125.800 same as CB-N*-CT, penalty score= 0.1
CR-NB-CV 70.000 117.000
H5-CR-NB 50.000 120.000
H4-CV-NB 50.000 120.000
H1-CT-H1 35.000 109.500
HC-CT-HC 35.000 109.500
C -CT-H1 50.000 109.500
DIHE
CC-CT-CT-NT 9 1.400 0.000 3.000
HC-CT-CT-NT 9 1.400 0.000 3.000
O -C -CT-NT 6 0.000 0.000 2.000
CT-CT-NT-H 6 1.800 0.000 3.000
H1-CT-NT-H 6 1.800 0.000 3.000
C -CT-NT-H 6 1.800 0.000 3.000
N*-CC-CT-CT 6 0.000 0.000 2.000
CV-CC-CT-CT 6 0.000 0.000 2.000
O -C -CT-CT 6 0.000 0.000 2.000
CT-CC-N*-CR 2 9.500 180.000 2.000 same as X -cd-nd-X , penalty score= 0.0
CT-CC-N*-CT 2 9.500 180.000 2.000 same as X -cd-nd-X , penalty score= 0.0
CT-CC-CV-NB 4 20.600 180.000 2.000
CT-CC-CV-H4 4 20.600 180.000 2.000
NB-CR-N*-CC 2 9.500 180.000 2.000 same as X -cd-nd-X , penalty score= 0.0
H5-CR-N*-CC 2 9.500 180.000 2.000 same as X -cd-nd-X , penalty score= 0.0
H1-CT-N*-CC 6 0.000 0.000 2.000
N*-CC-CV-NB 4 20.600 180.000 2.000
N*-CC-CV-H4 4 20.600 180.000 2.000
N*-CR-NB-CV 2 10.000 180.000 2.000
H1-CT-N*-CR 6 0.000 0.000 2.000
CC-CV-NB-CR 2 4.800 180.000 2.000
H4-CV-NB-CR 2 4.800 180.000 2.000
CV-CC-N*-CR 2 9.500 180.000 2.000 same as X -cd-nd-X , penalty score= 0.0
CV-CC-N*-CT 2 9.500 180.000 2.000 same as X -cd-nd-X , penalty score= 0.0
H5-CR-NB-CV 2 10.000 180.000 2.000
NB-CR-N*-CT 2 9.500 180.000 2.000 same as X -cd-nd-X , penalty score= 0.0
H5-CR-N*-CT 2 9.500 180.000 2.000 same as X -cd-nd-X , penalty score= 0.0
N*-CC-CT-HC 6 0.000 0.000 2.000
CV-CC-CT-HC 6 0.000 0.000 2.000
CC-CT-CT-H1 9 1.400 0.000 3.000
H1-CT-CT-HC 9 1.400 0.000 3.000
O -C -CT-H1 1 0.800 0.000 -1.000
O -C -CT-H1 1 0.000 0.000 -2.000
O -C -CT-H1 1 0.080 180.000 3.000
C -CT-CT-CC 9 1.400 0.000 3.000
C -CT-CT-HC 9 1.400 0.000 3.000
IMPROPER
CT-CV-CC-N* 1.1 180.0 2.0 Using the default value
CC-CR-N*-CT 1.1 180.0 2.0 Using the default value
H5-N*-CR-NB 1.1 180.0 2.0 Using the default value
CC-H4-CV-NB 1.1 180.0 2.0 Using the default value
NONBON
NT 1.8240 0.1700 same as N
H 0.6000 0.0157
CT 1.9080 0.1094
CC 1.9080 0.0860
N* 1.8993 0.0941 same as nc
CR 1.9080 0.0860
NB 1.8993 0.0941 same as nc
CV 1.9080 0.0860
H4 1.4090 0.0150
H5 1.3590 0.0150
H1 1.3870 0.0157
HC 1.4870 0.0157
C 1.9080 0.0860
O 1.6612 0.2100
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Received on Mon Jul 15 2024 - 23:30:02 PDT
