[gmx-users] AMBER atom type for Hydroxamate moeity

raja raja_28 at fastmail.us
Thu Nov 30 13:01:27 CET 2006

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 

 HO    ||
   \  /  \

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
amber99_36        14.01000      ; NB  sp2 N in 5 memb.ring w/LP
amber99_37        14.01000      ; NC  sp2 N in 6 memb.ring w/LP
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!
  raja_28 at fastmail.us

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