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 Wed Jun 28 2017 - 21:00:02 PDT
