Hi Ingso,
I agree with Dr. Horn, the atom type of the amide N of MHS was determined to be NT in the .ac file, which was correct based on the input structure but not the expected type for MHS as an embedded residue in protein (if it’s not at the N-terminal). You could manually change this in the .ac file.
Alternatively, adding a capping group to MHS in the initial residue structure can avoid the change of atom type like this. It’s common in the starting structure to cap the N terminal by C(=O)CH3 and the C terminal by [NH]CH3. You can always omit the additional atoms by processing it with a mainchain file.
Hope this helps!
From: Ingso Limbu via AMBER <amber.ambermd.org>
Date: Monday, July 15, 2024 at 11:26 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] C termini does not seem be read as CT in tleap
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 Wed Jul 17 2024 - 13:30:01 PDT
