[gmx-users] AMBER atom type for Hydroxamate moeity

Mark Abraham Mark.Abraham at anu.edu.au
Thu Nov 30 13:12:10 CET 2006

raja wrote:
> 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

Your N has an unsatisfied valence... what's missing? (Don't bother to 
tell me, it doesn't matter)

> 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. 

Probably, none of them. Force fields are not magic numbers that can be 
applied to all possible "types" of atoms. They are constructs designed 
to be reliably applicable to fairly narrow sets of atom types under the 
range of conditions they were parametrized with (also normally narrow). 
You will see this when you read the paper that describes the development 
process of this force field. Notwithstanding, people routinely abuse 
them with gay abandon, probably on the bad advice of others, or their 
own experience of the fairly good transferability of quantum-chemical 

Your only vaguely reliable course is to find a set of experimental data 
consistent with those used for the development of the force field, work 
out what new values you need to derive and to follow a process to 
optimize those values to reproduce the experimental data. This process 
is not for the inexperienced, or for the faint of heart.

Otherwise, you'll have the usual expensive random number generator.


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