Quoting Eduardo Mendez <pckboy.gmail.com>:
> I was wondering if anyone could share the amber parameter files for
> oxalate. I did gaussian calculations to get the mulliken charges,
> however, to my dismay, gaussian gives me an isomer, which
> is not in the planar conformation one would expect it to be :(
> Any idea were can I find a library site other than
> http://pharmacy.man.ac.uk/amber/ ???
- Yes, I saw this 'strange' conformation. Just try to re-run the job
using higher basis sets with DFT + diffusion function(s)
(B3LYP/6-31+G** or even higher...), using also different initial
structures (planar & not planar). Now this conformation might be the
right one. This could be explained by the two negative charges which
would be too close if the structure is planar... Did you look at the
frequencies ? They are all positive. This means this a real minimum at
the theory level used.
- AMBER FFs use RESP charges, not mulliken charges.
- Using the data I sent you, use the .mol2 file to add the FF atom
type (very simple for oxalate: O2, C, C, O2). Then, generate a
torsional profile for the O-C-C-O dihedral with structures generated
every 30 deg. Get the Eqm and Emm energy values, and fit Emm to Eqm.
(We have FFParmDev that does the job, but it is not yet ready to be
released; I can do it but not now).
regards, Francois
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Received on Wed Sep 19 2007 - 06:07:31 PDT
