Dear Amber members,
The step 8 of MCPB tutorial（building a standard model）says,"If there are less than 5 residues between two ligating residues, the bridging residues between them could be represented by GLY residues while the whole chain are capped by ACE and NME as well. "
I dont understand what does it means.For example,each residue between ligand 454 and 458(455-457) should be represented by GLY residue,like 455 LEU->455GLY,but how to create 455GLY?
And I also has a ligand 398,ACE should be added before 398 or 454(I mean if each fragment should be capped by ACE and NME ,or the whole)?
I feel that I dont make things clear,so anywehre is unclear,just say it.
Look forward to your reply!
Best wishes.
wjli
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Received on Tue Apr 07 2015 - 02:30:03 PDT
