Hi,
I have been trying to parametrize 3_formylpyridine using antechamber. However when I do the hydrogen attached to the carbon of the formyl group is assigned the h4 atom type. This atom type is for aromatic hydrogens containing 4 electron withdrawing groups. I thought that maybe an extended delocalised system was causing this atom type error, but I tried with formaldehyde and got the same atom type for both of the hydrogens. Can you suggest why this is occurring?
The PDB I have used for my input into antechamber is shown below:
HEADER FPy
ATOM 1 C2 FPy 1 1.340 -0.064 1.675
ATOM 2 H9 FPy 1 2.027 0.675 1.264
ATOM 3 C1 FPy 1 0.203 -0.445 0.969
ATOM 4 H8 FPy 1 -0.019 -0.012 -0.002
ATOM 5 C3 FPy 1 -0.658 -1.392 1.518
ATOM 6 H10 FPy 1 -1.555 -1.711 0.991
ATOM 7 N7 FPy 1 -0.441 -1.966 2.717
ATOM 8 C4 FPy 1 0.663 -1.597 3.403
ATOM 9 H11 FPy 1 0.803 -2.083 4.368
ATOM 10 C5 FPy 1 1.567 -0.657 2.916
ATOM 11 C6 FPy 1 2.758 -0.303 3.731
ATOM 12 H12 FPy 1 3.456 0.430 3.342
ATOM 13 O13 FPy 1 2.981 -0.803 4.813
TER
END
Thanks
Michael Carter
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 29 2010 - 05:30:04 PDT
