On Tue, Apr 19, 2016, Anna Cebrian Prats wrote:
>
> I am new using amber14 with tools of amber15 and I have a protein that
> contains a heme group.
There are heme parameters in the contributed parameters database:
http://sites.pharmacy.manchester.ac.uk/bryce/amber (look under cofactors, use
the all-atom version.)
If you obtained your pdb file from the RCSB, the residue and atom names should
match those in the library, but you should check these. Note that the residue
name is HEM, not HEME. You will need to add a bond between the iron and the
histidine residue (assuming you have this sort of connection.) You won't
involve antechamber in this sort of preparation.
...good luck...dac
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Received on Tue Apr 19 2016 - 05:00:04 PDT
