Hi Canaan,
Your ligand should be included in the sidechain model, standard model and
also the large model. But it is complicated to perform the modeling in MCPB
using nonstandard residues. I recommend you to wait for the releasing of
AmberTools15, which has a MCPB.py program (a python version of MCPB) that
could help to do the modeling quickly. Its tutorial will also be online
then.
Hope that helps,
Pengfei
2015-04-27 3:42 GMT-04:00 chemjxn <chemjxn.126.com>:
> Hello,
> I want to parameterization zn2+. The complex contains a protein, a ligand,
> and a zn2+ ion. In the process of the parameterization, whether the ligand
> is parameterized with the protein and the zn2+ together or not. Please help
> me. Thank you very much!
>
>
> Best wishes!
> Canaan
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--
Pengfei Li
Ph.D. Candidate
Merz Research Group
Department of Chemistry
Michigan State University
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Received on Mon Apr 27 2015 - 07:00:03 PDT
