Hello,
I am trying to simulate N-methylglycine amide. I selected 'none'
for the termini using oplsaa forcefield. I got the topology but I got
the error saying:
ERROR 1 [file topol.top, line 126]:
No default Ryckaert-Bell. types
I checked the line 126 in my topol file and it is the dihedral between
the atoms C-C-C-N (5 1 9 7). This is my PDB file:
ATOM 1 CA NAGA 1 2.010 -3.420 3.690 1.00 20.00
C
ATOM 2 HA1 NAGA 1 2.621 -3.652 4.447 1.00 20.00
H
ATOM 3 HA2 NAGA 1 1.081 -3.720 3.908 1.00 20.00
H
ATOM 4 HA3 NAGA 1 2.321 -3.880 2.858 1.00 20.00
H
ATOM 5 CB NAGA 1 2.020 -1.900 3.470 1.00 20.00
C
ATOM 6 OB NAGA 1 2.720 -1.200 4.200 1.00 20.00
O
ATOM 7 NE NAGA 1 1.270 -1.350 2.500 1.00 20.00
N
ATOM 8 HE NAGA 1 1.280 -0.370 2.350 1.00 20.00
H
ATOM 9 CC NAGA 1 0.360 -2.060 1.560 1.00 20.00
C
ATOM 10 HC1 NAGA 1 -0.410 -1.462 1.336 1.00 20.00
H
ATOM 11 HC2 NAGA 1 0.020 -2.891 2.000 1.00 20.00
H
ATOM 12 CD NAGA 1 1.090 -2.440 0.270 1.00 20.00
C
ATOM 13 OD NAGA 1 2.270 -2.810 0.300 1.00 20.00
O
ATOM 14 NB NAGA 1 0.370 -2.340 -0.840 1.00 20.00
N
ATOM 15 HB1 NAGA 1 0.780 -2.570 -1.720 1.00 20.00
H
ATOM 16 HB2 NAGA 1 -0.580 -2.040 -0.790 1.00 20.00
H
Is there a way for me to determine that specific dihedral in .bon.itp file?
Nisha P
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