Dear Liping,
This is very interesting... I want to underline that the R.E.D.
program is specially designed for performing this type of work.
You first have to optimize this transition state structure and
correctly characterize its frequencies... Then, for this structure you
have to perform molecular electrostatic potential computation and then
charge fitting. I would carefully compare ESP vs RESP charges for the
Pd center in this case; see for instance this type of comparison for
Fe3+ complexes available in R.E.DD.B.:
http://q4md-forcefieldtools.org/REDDB/projects/F-88/
http://q4md-forcefieldtools.org/REDDB/projects/F-89/
R.E.D. Server and even R.E.D. Server Development can help you here as
well to generate a force field library for this transition state
structure; you could also generate a molecular fragment for this
transition state structure if needed. At the end R.E.D. generate a
force field library to the mol2 file format.
Then, once you have generated the force field library for this
transition state structure you have to define the force field atom
types; better performing this task manually (than using a tool to do
this task)... and obviously you have to write a specific frcmod file.
Here the key is "the angle values" in your transition state structure
around the palladium to define the atom types...
This email contains only generalities, but if you use R.E.D. Server
and provide its job 'PXXXX' name we will be happy to help if we can.
regards, Francois
> I want to use amber to parameterize a force field for a transition state
> of an organic molecule with transition metal-palladium.
> When I only defined one new atom type for palladium (in tleap and
> the frcmod file),
> it could run successfully. But when I defined more new atoms types
> in addition to
> palladium, such as nitrogen atom that bonded to palladium, it would
> run with error message.
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Received on Thu Feb 28 2013 - 23:00:02 PST
