Re: [AMBER] MCPB HEME

From: Marcos Serrou do Amaral <marcossamaral.gmail.com> Date: Mon, 11 Dec 2017 10:53:14 -0300

---
Marcos S.A.
On Mon, Dec 11, 2017 at 8:00 AM, Rana Rehan Khalid <rrkhalid.umich.edu>
wrote:
> Dear AMber users
>
> I follow the mcpb tutorial of heme metal containing protein. After that ran
> the system for minimization and i got the .rst file then i use
>
> ambpdb -p b-h.prmtop -c min.rst > pdbauto.pdb
>
>  to observe my system pdb in chimera visualization tool. Then I see That
> chimera show only two bond one fe------NO and other fe------NA (porphyrin
> nitrogen). It does not show the  rest 3 porphyrin bond with FE and one
> FE------HIS.
> Is there anything wrong. Yes i know the bond information in the prmtop
> file. And I can see bond after loading prmtop.  But why chimera detect the
> only 2 bond.
> I also uploaded the image of system.
> Kindly guide
>
> Thanks for yours Attentions.
>
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