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
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
MCPB.py. Now I want to check how this domain dynamics affect the adjacent
domain.
Best Regards
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
(image/png attachment: imageee.png)
