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1 year 4 months ago #9557
by Nada_TAIB
other molecules was created by Nada_TAIB
Dear all,
I would like to perform CG-simulation for a Clozapine (3-chloro-6-(4-methylpiperazin-1-yl)-11H-benzo[1,4]benzodiazepine) and POPC/Cholesterol bilayer (Martini 2). I tried to parametrize the clozapine molecule in Martini 2, . The energy minimization step keeps failing. Can anyone help me please?/
Clozapine mapping
CLZ
B1 SN0 0 N1 C1 C2 C5
B2 SN0 0 N2 C3 C4
B3 SN0 0 N3 C6 C7 C18
B4 SC5 0 C8 C9 Cl C10
B5 SNd 0 C11 C12 N4 C13
B6 SC5 0 C14 C15
B7 SC5 0 C16 C17
>bonds
1 2
2 3
3 4
4 5
4 6
5 3
5 6
6 7
3 7
>angles
1 2 3
3 4 5
4 5 3
4 5 6
5 3 4
2 3 7
3 7 6
>dihedrals
1 2 3 7
2 3 4 5
5 4 6 7
3 5 6 7
itp file
[ moleculetype ]
CLZ 1
[ atoms ]
1 SN0 1 CLZ B1 1 0
2 SN0 1 CLZ B2 2 0
3 SN0 1 CLZ B3 3 0
4 SC5 1 CLZ B4 4 0
5 SN0 1 CLZ B5 5 0
6 SC5 1 CLZ B6 6 0
7 SC5 1 CLZ B7 7 0
[ bonds ]
1 2 1 0.24470 3000
2 3 1 0.27400 3000
3 4 1 0.35810 1250
4 5 1 0.31050 3000
4 6 1 0.61560 3000
5 3 1 0.23490 3000
5 6 1 0.33600 3000
6 7 1 0.20690 3000
3 7 1 0.33720 3000
[ angles ]
1 2 3 1 169.5685 45
3 4 5 1 38.34410 45
4 5 3 1 82.81440 45
4 5 6 1 144.5860 45
5 3 4 1 58.84150 45
2 3 7 1 83.35440 45
3 7 6 1 88.42470 45
[ dihedrals ]
1 2 3 7 2 -42.507 45
2 3 4 5 2 132.82340 45
5 4 6 7 2 111.51 45
3 5 6 7 2 8.98570 45
[ constraints ]
[ exclusions ]
Thank you very much
I would like to perform CG-simulation for a Clozapine (3-chloro-6-(4-methylpiperazin-1-yl)-11H-benzo[1,4]benzodiazepine) and POPC/Cholesterol bilayer (Martini 2). I tried to parametrize the clozapine molecule in Martini 2, . The energy minimization step keeps failing. Can anyone help me please?/
Clozapine mapping
CLZ
B1 SN0 0 N1 C1 C2 C5
B2 SN0 0 N2 C3 C4
B3 SN0 0 N3 C6 C7 C18
B4 SC5 0 C8 C9 Cl C10
B5 SNd 0 C11 C12 N4 C13
B6 SC5 0 C14 C15
B7 SC5 0 C16 C17
>bonds
1 2
2 3
3 4
4 5
4 6
5 3
5 6
6 7
3 7
>angles
1 2 3
3 4 5
4 5 3
4 5 6
5 3 4
2 3 7
3 7 6
>dihedrals
1 2 3 7
2 3 4 5
5 4 6 7
3 5 6 7
itp file
[ moleculetype ]
CLZ 1
[ atoms ]
1 SN0 1 CLZ B1 1 0
2 SN0 1 CLZ B2 2 0
3 SN0 1 CLZ B3 3 0
4 SC5 1 CLZ B4 4 0
5 SN0 1 CLZ B5 5 0
6 SC5 1 CLZ B6 6 0
7 SC5 1 CLZ B7 7 0
[ bonds ]
1 2 1 0.24470 3000
2 3 1 0.27400 3000
3 4 1 0.35810 1250
4 5 1 0.31050 3000
4 6 1 0.61560 3000
5 3 1 0.23490 3000
5 6 1 0.33600 3000
6 7 1 0.20690 3000
3 7 1 0.33720 3000
[ angles ]
1 2 3 1 169.5685 45
3 4 5 1 38.34410 45
4 5 3 1 82.81440 45
4 5 6 1 144.5860 45
5 3 4 1 58.84150 45
2 3 7 1 83.35440 45
3 7 6 1 88.42470 45
[ dihedrals ]
1 2 3 7 2 -42.507 45
2 3 4 5 2 132.82340 45
5 4 6 7 2 111.51 45
3 5 6 7 2 8.98570 45
[ constraints ]
[ exclusions ]
Thank you very much
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