From: Rana Rehan Khalid <rrkhalid.umich.edu>
Date: Mon, 11 Dec 2017 16:00:11 +0500

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
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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(image/png attachment: mcbp.png)

Received on Mon Dec 11 2017 - 03:30:03 PST
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