[gmx-users] AMBER atom type for Hydroxamate moeity

Maik Goette mgoette at mpi-bpc.mpg.de
Thu Nov 30 14:52:18 CET 2006

Maybe, one could also think about calculating the RESP charges via QM, 
e.g. with Gaussian...Further parameters, like force-constants and 
dihedrals could also be evaluated...

But what's against an expensive random number generator?
I fear I'm doing this with FEP all day long...;)

Raja: We are (mostly) not doing LEGO here. You should inform yourself 
about the theoretic parts in general. Then you would see, that LEGOing a 
molecule can't be feasible....I suggest e.g. Leach, Molecular Modelling, 
Section 3: Empirical force field models.
There you can find lots of information about what MD in general resembles.

Best regards

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/

Mark Abraham wrote:
> 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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