Dear gmxions,
I am writing a topology for a ligand using AMBER99 force field
convention. The ligand contains the hydroxamate group, for your quick
reference I have drawn it below
O
HO ||
\ / \
N
Please let me know which atoms type in amber can be used for these
atoms.... Especially the Nitrogen atom in this group. Since I am using
carbonyl group and hydroxyl group atoms types for oxygen (But I am not
sure of its validity). Please help me to chose appropriate atoms type.
I also pasted available atom types for Nitrogen in AMBER99 force field.
amber99_34 14.01000 ; N sp2 nitrogen in amide groups
amber99_35 14.01000 ; NA sp2 N in 5 memb.ring w/H atom
(HIS)
amber99_36 14.01000 ; NB sp2 N in 5 memb.ring w/LP
(HIS,ADE,GUA)
amber99_37 14.01000 ; NC sp2 N in 6 memb.ring w/LP
(ADE,GUA)
amber99_38 14.01000 ; N2 sp2 N in amino groups
amber99_39 14.01000 ; N3 sp3 N for charged amino groups
(Lys, etc)
amber99_40 14.01000 ; N* sp2 N
With thanks!
B.Nataraj
--
raja
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