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发表于 2018-11-27 11:21:44
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Do you mean part of the protein denatured or it still holds the original structure but is just sticking out of the boundary. If it's the first case, there is definitely something funny about the structure. If it is the second case, you can do the following:
1. solvent the protein in the bigger water box (make sure you have at least 9-A water layer at any point wrapping about the protein
2. If the protein is not quite spherical, you might thinking of using irregular shape of water box and make sure everything is fully solvated and none of the protein atoms can see their image. |
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