Dear all amber users,
I'm studying a protein that has inosine as its substrate. I'm not getting amber to recognize inosine when I load the PDB file into tleap. I researched that amber has parameters for inosine, but I don't know how it recognizes the pdb.
The PDB I'm using is:
HETATM 1 C5' I 4 1 -13.592 13.948 17.001 0.00 0.00 C
HETATM 2 O5' I 4 1 -13.689 12.651 16.407 0.00 0.00 O
HETATM 3 C4' I 4 1 -13.720 15.139 16.027 0.00 0.00 C
HETATM 4 O4' I 4 1 -14.771 15.096 15.029 0.00 0.00 O
HETATM 5 C3' I 4 1 -14.043 16.386 16.848 0.00 0.00 C
HETATM 6 O3' I 4 1 -13.022 17.386 16.620 0.00 0.00 O
HETATM 7 C2' I 4 1 -15.490 16.785 16.468 0.00 0.00 C
HETATM 8 O2' I 4 1 -15.638 18.117 15.969 0.00 0.00 O
HETATM 9 C1' I 4 1 -15.990 15.789 15.420 0.00 0.00 C
HETATM 10 N1 I 4 1 -17.652 10.941 14.883 0.00 0.00 N
HETATM 11 C2 I 4 1 -17.055 11.743 13.979 0.00 0.00 C
HETATM 12 N3 I 4 1 -16.701 13.008 14.258 0.00 0.00 N
HETATM 13 C4 I 4 1 -16.937 13.538 15.500 0.00 0.00 C
HETATM 14 C5 I 4 1 -17.584 12.725 16.530 0.00 0.00 C
HETATM 15 C6 I 4 1 -17.936 11.351 16.132 0.00 0.00 C
HETATM 16 O6 I 4 1 -18.484 10.615 16.972 0.00 0.00 O
HETATM 17 N7 I 4 1 -17.700 13.473 17.637 0.00 0.00 N
HETATM 18 C8 I 4 1 -17.161 14.672 17.360 0.00 0.00 C
HETATM 19 N9 I 4 1 -16.730 14.709 16.084 0.00 0.00 N
END
Thanks,
Thamires
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Received on Tue Jul 20 2021 - 07:30:02 PDT
