[gmx-users] AMBER atom type for Hydroxamate moeity

[raja]

Hi Goette,
Thanks for your mail. I have just find an article done a similar
work...I am trying to reach them to get their parameters. Unfortunately
I am not having Gaussian. Can you suggest me some other freely available
quantum mechanics software ?

This reference article : "Binding affinity of hydroxamate inhibitors of
matrix metalloproteinase-2 "
                          Volume 10, Number 2 / April, 2004

B.Nataraj




On Thu, 30 Nov 2006 14:52:18 +0100, "Maik Goette"
<mgoette at mpi-bpc.mpg.de> said:
> 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
> Germany
> Tel.  : ++49 551 201 2310
> Fax   : ++49 551 201 2302
> Email : mgoette[at]mpi-bpc.mpg.de
>          mgoette2[at]gwdg.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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> > .
> > 
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-- 
  raja
  raja_28 at fastmail.us

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