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pymol_align_protein_ca
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@ndonyapour
ndonyapour committed Dec 18, 2024
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Showing 1 changed file with 3 additions and 96 deletions.
99 changes: 3 additions & 96 deletions utils/pre-process/structure-change/append-ligand-tool/tests/pep_ligand.itp
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[ moleculetype ]
;name nrexcl
PEP 3

[ atoms ]
; nr type resi res atom cgnr charge mass ; qtot bond_type
1 p5 1 PEP P 1 1.353905 30.97000 ; qtot 1.354
2 o 1 PEP O1P 2 -0.934168 16.00000 ; qtot 0.420
3 o 1 PEP O2P 3 -0.934168 16.00000 ; qtot -0.514
4 o 1 PEP O3P 4 -0.934168 16.00000 ; qtot -1.449
5 o 1 PEP O2' 5 -0.908301 16.00000 ; qtot -2.357
6 c 1 PEP C1 6 0.891801 12.01000 ; qtot -1.465
7 o 1 PEP O1 7 -0.908301 16.00000 ; qtot -2.373
8 ce 1 PEP C2 8 0.260900 12.01000 ; qtot -2.112
9 os 1 PEP O2 9 -0.472500 16.00000 ; qtot -2.585
10 c2 1 PEP C3 10 -0.546001 12.01000 ; qtot -3.131
11 ha 1 PEP H32 11 0.065500 1.00800 ; qtot -3.066
12 ha 1 PEP H31 12 0.065500 1.00800 ; qtot -3.000

[ bonds ]
; ai aj funct r k
1 2 1 1.4866e-01 4.0125e+05 ; P - O1P
1 3 1 1.4866e-01 4.0125e+05 ; P - O2P
1 4 1 1.4866e-01 4.0125e+05 ; P - O3P
1 9 1 1.6147e-01 2.7665e+05 ; P - O2
5 6 1 1.2183e-01 5.3363e+05 ; O2' - C1
6 7 1 1.2183e-01 5.3363e+05 ; C1 - O1
6 8 1 1.4825e-01 2.9665e+05 ; C1 - C2
8 9 1 1.3710e-01 3.1372e+05 ; C2 - O2
8 10 1 1.3461e-01 4.5798e+05 ; C2 - C3
10 11 1 1.0879e-01 2.8711e+05 ; C3 - H32
10 12 1 1.0879e-01 2.8711e+05 ; C3 - H31

[ pairs ]
; ai aj funct
1 6 1 ; P - C1
1 10 1 ; P - C3
2 8 1 ; O1P - C2
3 8 1 ; O2P - C2
4 8 1 ; O3P - C2
5 9 1 ; O2' - O2
5 10 1 ; O2' - C3
6 11 1 ; C1 - H32
6 12 1 ; C1 - H31
7 9 1 ; O1 - O2
7 10 1 ; O1 - C3
9 11 1 ; O2 - H32
9 12 1 ; O2 - H31

[ angles ]
; ai aj ak funct theta cth
1 9 8 1 1.2318e+02 6.4986e+02 ; P - O2 - C2
2 1 3 1 1.1580e+02 3.8351e+02 ; O1P - P - O2P
2 1 4 1 1.1580e+02 3.8351e+02 ; O1P - P - O3P
2 1 9 1 1.1546e+02 3.6694e+02 ; O1P - P - O2
3 1 4 1 1.1580e+02 3.8351e+02 ; O2P - P - O3P
3 1 9 1 1.1546e+02 3.6694e+02 ; O2P - P - O2
4 1 9 1 1.1546e+02 3.6694e+02 ; O3P - P - O2
5 6 7 1 1.3025e+02 6.5220e+02 ; O2' - C1 - O1
5 6 8 1 1.2320e+02 5.7597e+02 ; O2' - C1 - C2
6 8 9 1 1.1467e+02 5.7421e+02 ; C1 - C2 - O2
6 8 10 1 1.2042e+02 5.4769e+02 ; C1 - C2 - C3
7 6 8 1 1.2320e+02 5.7597e+02 ; O1 - C1 - C2
8 10 11 1 1.2045e+02 4.1430e+02 ; C2 - C3 - H32
8 10 12 1 1.2045e+02 4.1430e+02 ; C2 - C3 - H31
9 8 10 1 1.2370e+02 5.8693e+02 ; O2 - C2 - C3
11 10 12 1 1.1690e+02 3.1890e+02 ; H32 - C3 - H31

[ dihedrals ] ; propers
; for gromacs 4.5 or higher, using funct 9
; i j k l func phase kd pn
1 9 8 6 9 180.00 4.39320 2 ; P- O2- C2- C1
1 9 8 10 9 180.00 7.32200 2 ; P- O2- C2- C3
2 1 9 8 9 0.00 3.34720 2 ; O1P- P- O2- C2
3 1 9 8 9 0.00 3.34720 2 ; O2P- P- O2- C2
4 1 9 8 9 0.00 3.34720 2 ; O3P- P- O2- C2
5 6 8 9 9 180.00 9.10020 2 ; O2'- C1- C2- O2
5 6 8 10 9 180.00 9.10020 2 ; O2'- C1- C2- C3
6 8 10 11 9 180.00 27.82360 2 ; C1- C2- C3- H32
6 8 10 12 9 180.00 27.82360 2 ; C1- C2- C3- H31
7 6 8 9 9 180.00 9.10020 2 ; O1- C1- C2- O2
7 6 8 10 9 180.00 9.10020 2 ; O1- C1- C2- C3
9 8 10 11 9 180.00 27.82360 2 ; O2- C2- C3- H32
9 8 10 12 9 180.00 27.82360 2 ; O2- C2- C3- H31

[ dihedrals ] ; impropers
; treated as propers in GROMACS to use correct AMBER analytical function
; i j k l func phase kd pn
6 10 8 9 4 180.00 4.60240 2 ; C1- C3- C2- O2
8 5 6 7 4 180.00 4.60240 2 ; C2- O2'- C1- O1
8 11 10 12 4 180.00 4.60240 2 ; C2- H32- C3- H31

; Include Position restraint file
#ifdef POSRES_LIG
#include "posre_PEP-H.itp"
#endif
version https://git-lfs.github.com/spec/v1
oid sha256:a5f530e19fdd2d9cd0185a7f8448fe4a3de2658defa5392bfa4529191af484a2
size 5370

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