Andrew its the ferrous ii oxidation state
On Wed, Jun 28, 2017 at 11:55 PM, Andrew Schaub <aschaub.uci.edu> wrote:
> Follow the MCPB Heme tutorial:
>
> http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm
>
>
> It walks you through paramterizing your heme and iron. Metals complicate
> things. Heme is complicated further by the high and low spin states, the
> multiple intermediates and the multiple oxidation states of the iron. so
> extra care has to be taken to set these systems up. You need to know what
> oxidation state your iron is in that you want to simulate: II, III, IV. You
> need to know its soin, its net charge, and oxidation state.
>
>
> What intermediate state are you looking at?
>
>
> Andrew
>
> On Wed, Jun 28, 2017 at 15:44 Rana Rehan Khalid <rrkhalid.umich.edu>
> wrote:
>
> > hi Everyone
> >
> > i used antechamber for my heme fe--o2 ligand it show this error and mol2
> > not formed for heme-fe----O2. i also sending you the leap.log kindly tell
> > me where i am wrong
> >
> > Running: /home/rehan/Downloads/amber16/bin/bondtype -j full -i
> > ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
> >
> > For atom[26]:O01, the best APS is not zero, bonds involved by this atom
> are
> > frozen
> >
> > For atom[45]:Fe, the best APS is not zero, bonds involved by this atom
> are
> > frozen
> >
> > The frozen atom type can only be 1, 2, 3, 7 (aromatic single), 8
> (aromatic
> > double)Error: cannot run "/home/rehan/Downloads/amber16/bin/bondtype -j
> > full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
> > judgebondtype() of antechamber.c properly, exit
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Received on Thu Jun 29 2017 - 14:30:02 PDT
