There are no charges, but those will be added at a later step using MCPB,
after the QM calculations. It is weird about the atom types, but I would
use the .mol2 file that Prof Case generated for you with the gaff atom
types (n1 and o). Ensure that when you do the QM charges that NO is bound
to your heme, and ensure you are using the right multiplicity and oxidation
state (Fe2+) for the complex. Your iron should be coordinated to six
nitrogen atoms total (one from imidazole, one from NO, and four from the
heme). Nitric oxide by itself would be a doublet I believe, but in
combination with heme, I'm not sure what the multiplicity of that species
is (low spin vs high spin).
Andrew
On Wed, Jul 5, 2017 at 9:19 AM, David A Case <david.case.rutgers.edu> wrote:
> On Wed, Jul 05, 2017, Rana Rehan Khalid wrote:
> > >
> > > > I use this command to convert NITRIC OXIDE containing pdb file to
> mol2
> > > >
> > > > antechamber -fi pdb -fo mol2 -i NIT.pdb -o NIT.mol2 -pf y
>
> I can't reproduce your result. I've attached the mol2 file I get with the
> above command.
>
> Be sure that the antechamber tests are passing with your installation. I
> used
> AmberTools17, but nothing has changed from AmberTools16 that should be
> relevant here. Probably worth double-checking your run.
>
> Maybe someone else on the list has seen all of the atom types get replaced
> with the residue name, and can chime in here.
>
> ....dac
>
>
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>
>
--
Andrew Schaub
Graduate Program in Chemical & Structural Biology
Tsai Lab, http:///www.tsailabuci.com/ <http://www.tsailabuci.com/>
Luo Lab, http://rayl0.bio.uci.edu/html/
University of California, Irvine
Irvine, CA 92697-2280
949-824-8829 (lab)
949-877-9380 (cell)
aschaub.uci.edu <http://www.linkedin.com/pub/andrew-schaub/9a/907/382/>
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Received on Wed Jul 05 2017 - 10:00:02 PDT
