liuyansong 发表于 2025-12-16 13:57
谢谢老师回答，如果这一块没错的话。我在生成复合物拓扑文件的时候，在运行到这一段代码“saveamberparm mo ...

没完整leap input无法判断。

运行tleap时是否source了适当文件才load pdb？

加载各力场文件是否齐全？e.g. frcmod的loadberparams、如果ligand参数存了个lib文件loadoff 该lib文件......

我自己跑完parmchk2会先转个ligand 的lib，如

1. source leaprc.protein.ff14SB
   
2. source leaprc.gaff
   
3. mods = loadamberparams LIG_AC.frcmod
   
4. LIG = loadmol2 LIG_AC.mol2
   
5. check LIG
   
6. savepdb LIG LIG_AC.pdb
   
7. saveoff LIG LIG_AC.lib

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然后才跑Complex的tleap

1. source leaprc.protein.ff14SB
   
2. source leaprc.water.tip3p
   
3. source leaprc.gaff
   
4. loadamberparams  LIG_AC.frcmod
   
5. loadoff LIG_AC.lib
   
6. 
   
7. com = loadpdb complex_fixed.pdb
   
8. prot = loadpdb protein_fixed.pdb
   
9. lig = loadpdb ligand_fixed.pdb
   
10. 
    
11. saveamberparm com complex.prmtop complex.inpcrd
    
12. saveamberparm prot protein.prmtop protein.inpcrd
    
13. saveamberparm lig ligand.prmtop ligand.inpcrd
    
14. 
    
15. solvateoct com TIP3PBOX 10.0
    
16. charge com
    
17. addions com Na+ 0
    
18. addions com Cl- 0
    
19. saveamberparm com complex_solvated.prmtop complex_solvated.inpcrd
    
20. quit

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(以上是我几年前跑Amber16的脚本，现在最Amber建议用的是FF19SB+GAFF2+OPC)

不是缺少参数，而是这些参数在标准力场文件中已经有了，parmchk2不需要再为这些参数拟合。下面是Amber官网的教程描述：The parmchk2 program figures out what parameters will be needed and checks to see if they are in the standard files. If not, it tries to make educated guesses, and puts these new parameters into a file we are calling "frcmod.cro" here.

谢谢老师回答，如果这一块没错的话。我在生成复合物拓扑文件的时候，在运行到这一段代码“saveamberparm mol complex.prmtop complex.inpcrd”不知道什么原因报错了说是识别不了原子类型。下面是报错信息/opt/amber24/bin/teLeap: Warning!
The unperturbed charge of the unit (-13.614100) is not zero.
FATAL:  Atom .R<LEU 455>.A<OXT 20> does not have a type.
FATAL:  Atom .R<Lig 457>.A<C 1> does not have a type.
FATAL:  Atom .R<Lig 457>.A<C1 2> does not have a type.
FATAL:  Atom .R<Lig 457>.A<C2 3> does not have a type.
FATAL:  Atom .R<Lig 457>.A<C3 4> does not have a type.
FATAL:  Atom .R<Lig 457>.A<C4 5> does not have a type.
FATAL:  Atom .R<Lig 457>.A<C5 6> does not have a type.
FATAL:  Atom .R<Lig 457>.A<C6 7> does not have a type.
FATAL:  Atom .R<Lig 457>.A<C7 8> does not have a type.
FATAL:  Atom .R<Lig 457>.A<C8 9> does not have a type.
FATAL:  Atom .R<Lig 457>.A<C9 10> does not have a type.
FATAL:  Atom .R<Lig 457>.A<C10 11> does not have a type.
FATAL:  Atom .R<Lig 457>.A<H 12> does not have a type.

非常感谢老师的回答，如果这里是正常的话到最后生成复合物拓扑文件的时候总是报错，无法识别小分子的原子类型。我是跟着这个网址一直按部就班的做的https://blog.csdn.net/2201_75400172/article/details/151613248。到第五步生成拓扑文件运行到这一串代码“saveamberparm mol complex.prmtop complex.inpcrd”时候开始报错了

frcmod 那些是力场没有额外补充加上的，没有的项目就是力场已有不用补充。