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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