Re: [AMBER] How to show double bond connection between N=O2

From: Bill Ross <>
Date: Sat, 14 Oct 2017 15:47:40 -0700

The image making software would not know about double bond from the
amber prmtop, since only leap keeps track of bond order for its internal
use, and it is not included in the prmtop file.


On 10/14/17 7:31 AM, Rana Rehan Khalid wrote:
> Here is active site connections (bonds) of heme that is also bonded with
> Histidine at its one side (proximal) and other distal side connected with
> NO. FE bonded with Nitrogen with single bond and Nitrogen bonded with
> Oxygen with double bond. I want to know. How i can show double bond
> connection between nitrogen and Oxygen. Is it necessary or i can go for
> simulation with the same structure as given in the image kindly guide.
> mol = loadpdb no_mcpbpy.pdb
> bond mol.105.NE2 mol.188.FE ......Histidine
> bond mol.187.NA mol.188.FE .......heme
> bond mol.187.NB mol.188.FE ........heme
> bond mol.187.ND mol.188.FE ........heme
> bond mol.187.NC mol.188.FE..........heme
> bond mol.188.FE mol.189.N01.........Nitrogen
> bond mol.104.C mol.105.N
> bond mol.105.C mol.106.N
> Kind Regards
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Received on Sat Oct 14 2017 - 16:00:03 PDT
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