[gmx-users] AMBER atom type for Hydroxamate moeity

raja raja_28 at fastmail.us
Thu Nov 30 14:37:45 CET 2006

Thanks Mark for your reply. And sorry about missing one hydrogen in my
drawn topology...


On Thu, 30 Nov 2006 23:12:10 +1100, "Mark Abraham"
<Mark.Abraham at anu.edu.au> said:
> 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 
> methods.
> 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.
> Mark
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  raja_28 at fastmail.us

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