From: Jorgen Simonsen <>
Date: Sat, 26 Feb 2011 13:37:58 +0100

Well that is a good question i used the Mertz kollmann charges within
turbomole given those vdw radii - i have seen this parametrization
done before using diffuse functions on the metal center and 6-31g* on
the rest with dft

I Think my trouble is that amber somehow does not recognize my
hydrogens as tip3p maybe i should put in a vdw potential for Them?

On Saturday, February 26, 2011, FyD <> wrote:
> Jorgen,
> Did you correctly derive the charges/build the FF library for your
> metal center?
> regards, Francois
>> I look through and set the sp2 so now it is planar. After generating
>> the prmtop and inpcrd file and then getting pdb file using "ambpdb"
>> the starting structure looks fine meaning it looks like the optimized
>> input coordinates.
>> So my new trouble starts when I minimize in vacuum - so one of the
>> coordinating molecules is a water molecule where I have taken the
>> parameters from TIP3P - for the interaction I have defined a bond
>> between oxygen of water and the metal ion as some angles but when I
>> minimize the complex the proton nearest to the histidine merges with
>> it and the electrostatic potential explodes. The energy becomes
>> ********* and in the minimized structure NE2 and H from water have the
>> same coordinates. So how to prevent this - the nonbonded interaction
>> is 0.000 for water hydrogen so from the parameters define I cannot see
>> why this should not happen? In general what keep protons from water
>> from aligning with negative charged molecules?
>> Thanks
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Received on Sat Feb 26 2011 - 05:00:02 PST
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