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

Dear Rana,

Did you use parmed to double check that you have these bounds? If your
answer is YES, you should ask for Chimera Group and you can go to next
stage of your simulation.

Marcos S.A.
On Mon, Dec 11, 2017 at 8:00 AM, Rana Rehan Khalid <>
> 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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Received on Mon Dec 11 2017 - 06:00:04 PST
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