标题: 关于Amber原子名字总是出错问题请教 [打印本页] 作者Author: ShineZhu 时间: 2022-5-27 09:22 标题: 关于Amber原子名字总是出错问题请教 大家好：
我最近在开始学习Amber，然后初学我总是遇到残基名字报错的问题，想请教下这类问题的根本原因是什么。我直接拿用AF2预测的模型来跑模拟，然后在loadpdb就报错，然后我去看了ff19SB力场文件里的残基名字，发现在它支持的残基名字列表里，不仅HD1不支持，在我的PDB里还有HD2也没有存在，那为什么它只报错HD1呢？然后应该如何修改避免这种情况呢？手动修改这么多残基名字还是有其他方式可以避免残基命名错误问题呢？谢谢
> N559=loadpdb N559.pdb
Loading PDB file: ./N559.pdb
Created a new atom named: H within residue: .R<NMET 1>
Created a new atom named: HD1 within residue: .R<HIE 28>
Created a new atom named: HD1 within residue: .R<HIE 111>
Created a new atom named: HD1 within residue: .R<HIE 146>
Created a new atom named: HD1 within residue: .R<HIE 243>
Created a new atom named: HD1 within residue: .R<HIE 246>
Created a new atom named: HD1 within residue: .R<HIE 273>
Created a new atom named: HD1 within residue: .R<HIE 317>
Created a new atom named: HD1 within residue: .R<HIE 400>
Created a new atom named: HD1 within residue: .R<HIE 435>
Created a new atom named: HD1 within residue: .R<HIE 532>
Created a new atom named: HD1 within residue: .R<HIE 535>
Created a new atom named: HD1 within residue: .R<HIE 562>
total atoms in file: 8317
Leap added 13 missing atoms according to residue templates:
13 H / lone pairs
The file contained 13 atoms not in residue templates
Warning: Since the number of added atoms equals the number of missing atoms, it is likely
that some atoms had incorrect names; you may want to use addPdbAtomMap to map
these names, or change the names in the PDB file.