From: Jorgen Simonsen <>
Date: Sat, 26 Feb 2011 09:19:37 +0100


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?


On Fri, Feb 25, 2011 at 4:20 AM, David Case <> wrote:
> On Feb 24, 2011, at 6:18 PM, Jorgen Simonsen <> wrote:
>> and thanks for the response so I am adding a copper ion to a histidine
>> and as it might have other interactions with nearby residues I have
>> changed the type of NE2 to UA - yhe problem is that when I have
>> generate the inpcrd and prmtop and look at the pdb file(ambpdb from
>> ambertools) the imidazole ring has lost its planarity - having a boat
>> shape.
> Did you do a minimization or anything?  When you "generate the inpcrd" in tleap, it is just using whatever coordinates you give it.
> You might also check to see if you are missing any improper terms that would ordinarily keep planarity about the NE2 atom.
> ....dac
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Received on Sat Feb 26 2011 - 00:30:02 PST
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