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柳伊妃铁杆木虫 (小有名气)
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[求助]
amber模拟受体-配体复合物报错，小分子力场问题
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用amber模拟受体配体复合物出错，麻烦各位大神看看究竟是什么问题，如何解决呢？ > com = loadpdb gcx171.pdb Loading PDB file: ./gcx171.pdb -- residue 0: duplicate [ C] atoms (total 18) -- residue 0: duplicate [ H] atoms (total 2) -- residue 0: duplicate [ N] atoms (total 5) -- residue 0: duplicate [ O] atoms (total 2) Warning: Atom names in each residue should be unique. (Same-name atoms are handled by using the first occurrence and by ignoring the rest. Frequently duplicate atom names stem from alternate conformations in the PDB file.) Bond: Maximum coordination exceeded on .R<UNK 0>.A<H3 7> -- setting atoms pert=true overrides default limits ATOMS NOT BONDED: .R<UNK 0>.A<C 4> .R<UNK 0>.A<H3 7> !FATAL ERROR---------------------------------------- !FATAL: In file [atom.c], line 445 !FATAL: Message: bondAtomProblem found ! !ABORTING. |
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