From: case <>
Date: Sat, 26 Feb 2011 09:25:25 -0500

On Sat, Feb 26, 2011, Jorgen Simonsen wrote:
> 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.

This is still very weird. I suspect that I don't understand what you are
doing, and am missing something in your very limited description. Running
a molecule through tleap and saveAmberParm doesn't change the input
coordinates: if you have a boat shape at the end, you must have had a boat
shape at the beginning. It doesn't depend on whether the parameters are good
ones or bad ones, whether the atoms are known or unknown, etc.

> 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.

Are you using SHAKE for the water? Is there the "extra" H-H bond in water
that the TIP3P parameters assume? Both of these are required if you use the
parameters for TIP3P water. (It's the Lennard-Jones parameters of the oxygen
that keeps the hydrogens from merging with nearby molecules.


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Received on Sat Feb 26 2011 - 06:30:02 PST
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