From: FyD <>
Date: Sat, 26 Feb 2011 09:51:09 +0100


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

AMBER mailing list
Received on Sat Feb 26 2011 - 01:00:02 PST
Custom Search