Ingso,
I think the atom types in the MHS parameter definition are not correct,
i.e. the nitrogen should be N, not NT.
Since MHS is a modified alpha-amino acid, it should use the same atom
type as the other amino acids, and C is the standard atom type (and
name) for the carbon within the peptide bond, and N is the standard atom
type (and name) for the nitrogen in the peptide bond.
Thus, I suggest to change the atom type in your MHS prepin file from NT
to N (and maybe the name of H2 to H for the hydrogen in the peptide
bond, to be even more consistent; but that's only cosmetics).
Hope that helps.
Best,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
Am 16.07.2024 um 08:26 schrieb Ingso Limbu via AMBER:
> 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 Tue Jul 16 2024 - 01:30:02 PDT
