[AMBER] MCPB.py how to insert the heteroatom heme in the one domain of macromolecule

From: Rana Rehan Khalid <rrkhalid.umich.edu>
Date: Thu, 30 Nov 2017 19:44:54 +0500

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

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
MCPB.py. Now I want to check how this domain dynamics affect the adjacent

Best Regards

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Received on Thu Nov 30 2017 - 07:00:02 PST
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