Re: [AMBER] how to insert the heteroatom heme in the one domain of macromolecule

From: Pengfei Li <>
Date: Mon, 4 Dec 2017 16:22:19 -0600

Hi Rana,

It is a question outside the scope of But I think you can use cpptraj to align the single domain structure (which has HEME coordinates) you already have to part of structure with eight domains and then output the single domain structure after alignment. The HEME coordinates inside the output can help you estimate the HEME group coordinates in the structure of eight domains. See the “RMSD to Reference with Different Topology” part in this tutorial: <>.

Best regards,

> On Nov 30, 2017, at 8:44 AM, Rana Rehan Khalid <> wrote:
> Dear Amber users
> I predicted the macromolecule structure through density fitting. This
> structure consist of Eight domains. Now I want to insert the heme ligand
> among one of these domains. The structure of this heme containing domain is
> experimentally solved, I can model one domain by using that experimental
> structure and get the heme containing domain. But how I can insert or cat
> the heme in the one domain which is the part of whole protein (8 domain
> not separate domain) structure.
> I try to do this by using these command but heme remain separate from the
> structure definitely due to different coordinate positioning. Kindly guide
> me.
> cat Protein_H_renum.pdb HEM_H_renum.pdb FE.pdb NIT_H_renum.pdb | awk
> '$1!="END"' > SGC_H.pdb
> Sir I already done so much work on this heme containing domain using
> Now I want to check how this domain dynamics affect the adjacent
> domain.
> Best Regards
> <imageee.png>_______________________________________________
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Received on Mon Dec 04 2017 - 14:30:03 PST
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