Dear Amber,
When I used Amber to process the metal multi-copper oxidase, I saw two crystal water oxygen O1 and O2 binded with copper ions in the protein structure, as shown in red in the figure, and the structure fragment information is as follows:
HETATM 4210 CU CU A 601 -33.513 21.218 -4.759 1.00 21.28 Cu
HETATM 4211 CU CU A 602 -34.609 30.985 -13.514 1.00 15.38 Cu
HETATM 4212 CU CU A 603 -38.943 30.175 -11.542 1.00 16.86 Cu
HETATM 4213 CU CU A 604 -37.270 33.388 -11.656 1.00 19.02 Cu
HETATM 4214 O1 OXY A 605 -36.905 30.873 -12.306 1.00 7.73 O
HETATM 4215 O2 OXY A 605 -37.023 30.208 -12.729 1.00 23.19 O
I try to solve the issue using MCPB.py according to the amber list solution, but it failure.
How to use MCPB.py to generate OH parameters
http://archive.ambermd.org/201703/0167.html
How to generate coordinate and parameter files of O1 and O2? Are there any tutorials available? If anyone can provide any solutions, it would be greatly appreciated!
Best wishes,
Zhihong Xin,
NJAU university
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Received on Tue Dec 28 2021 - 05:00:02 PST
