在使用AmberTools25进行力场设置时，使用脚本出现报错

ZiJieXia

脚本如下：# tleap.in
source leaprc.protein.ff19SB

#添加铁原子定义
addAtomTypes {
   { "FE" "Fe" "sp0" }
}

# 把 hem.mol2 当“prep”加载进来
loadoff hem.lib

# 加载 GAFF2 参数
loadAmberParams hem.frcmod

# 读入你的 PDB
system = loadpdb protonatedTlnA.pdb

#删除氢
removeH system

#添加氢
addH system

#检查和添加电荷
charge system

# （可选）加水盒、离子…
source leaprc.water.tip3p
solvateBox system TIP3PBOX 10.0
addIons system Na+ 0
addIons system Cl- 0

# 输出拓扑和坐标
saveAmberParm system TlnA_ff19.prmtop TlnA_ff19.inpcrd
quit
命令和报错如下：
(AmberTools25) -bash-5.0$ tleap -f tleap.in
-I: Adding /home/XZJ/miniconda3/envs/AmberTools25/dat/leap/prep to search path.
-I: Adding /home/XZJ/miniconda3/envs/AmberTools25/dat/leap/lib to search path.
-I: Adding /home/XZJ/miniconda3/envs/AmberTools25/dat/leap/parm to search path.
-I: Adding /home/XZJ/miniconda3/envs/AmberTools25/dat/leap/cmd to search path.
-f: Source tleap.in.

Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./tleap.in
----- Source: /home/XZJ/miniconda3/envs/AmberTools25/dat/leap/cmd/leaprc.protein.ff19SB
----- Source of /home/XZJ/miniconda3/envs/AmberTools25/dat/leap/cmd/leaprc.protein.ff19SB done
Log file: ./leap.log
Loading parameters: /home/XZJ/miniconda3/envs/AmberTools25/dat/leap/parm/parm19.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA + ff19SB
Loading parameters: /home/XZJ/miniconda3/envs/AmberTools25/dat/leap/parm/frcmod.ff19SB
Reading force field modification type file (frcmod)
Reading title:
ff19SB AA-specific backbone CMAPs for protein 07/25/2019
Loading library: /home/XZJ/miniconda3/envs/AmberTools25/dat/leap/lib/amino19.lib
Loading library: /home/XZJ/miniconda3/envs/AmberTools25/dat/leap/lib/aminoct12.lib
Loading library: /home/XZJ/miniconda3/envs/AmberTools25/dat/leap/lib/aminont12.lib

/home/XZJ/miniconda3/envs/AmberTools25/bin/teLeap: Warning!
atom type FE - unknown hybridization sp0
Loading library: ./hem.lib
Loading parameters: ./hem.frcmod
Reading force field modification type file (frcmod)
Reading title:
Ferric-high-spin.frcmod- Shahrokh,K; Orendt,A; Yost, G.S; and Cheatham III, T.E. Jour Comp Chem (2011)
Loading PDB file: ./protonatedTlnA.pdb
Created a new atom named: HD1 within residue: .R<HIE 4>
Created a new atom named: HD1 within residue: .R<HIE 17>
Created a new atom named: HD1 within residue: .R<HIE 113>
Created a new atom named: HD1 within residue: .R<HIE 266>
Created a new atom named: HD1 within residue: .R<HIE 290>
Created a new atom named: HD1 within residue: .R<HIE 332>
Created a new atom named: HD1 within residue: .R<HIE 348>
Created a new atom named: HD1 within residue: .R<HIE 356>
Created a new atom named: HD1 within residue: .R<HIE 362>
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-NB-FE-*
+--- With Sp3 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-NA-FE-*
+--- With Sp3 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-ND-FE-*
+--- With Sp3 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-NC-FE-*
+--- With Sp3 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
  total atoms in file: 6532
  Leap added 1 missing atom according to residue templates:
       1 H / lone pairs
  The file contained 9 atoms not in residue templates

/home/XZJ/miniconda3/envs/AmberTools25/bin/teLeap: Fatal Error!
Error from the parser:
       syntax error.
       Check for typos, misspellings, etc.
       Try help on the command name and desc on the command arguments.

Exiting LEaP: Errors = 1; Warnings = 1; Notes = 0.

检查过很多地方了，比如大小写等等，但是始终报错，用的hem.lib和hem.frcmod下载地址：PCPD/HEM.frcmod at main · JiangLab2020/PCPD · GitHub，求助各位大佬

Lecly

1. > removeH
   
2. 
   
3. Error: Error from the parser:
   
4.        syntax error.
   
5.        Check for typos, misspellings, etc.
   
6.        Try help on the command name and desc on the command arguments.
   
7. 
   
8. > help
   
9. Help is available on the following subjects:
   
10. 
    
11. _cmd_options_       _types_             add                 addAtomTypes
    
12. addH                addIons             addIons2            addIonsRand
    
13. addPath             addPdbAtomMap       addPdbResMap        alias
    
14. alignAxes           bond                bondByDistance      center
    
15. charge              check               clearPdbAtomMap     clearPdbResMap
    
16. clearVariables      combine             copy                createAtom
    
17. createParmset       createResidue       createUnit          crossLink
    
18. debugOff            debugOn             debugStatus         deleteBond
    
19. deleteOffLibEntry   deleteRestraint     desc                deSelect
    
20. displayPdbAtomMap   displayPdbResMap    edit                flip
    
21. groupSelectedAtoms  help                impose              list
    
22. listOff             loadAmberParams     loadAmberPrep       loadMol2
    
23. loadMol3            loadOff             loadPdb             loadPdbUsingSeq
    
24. logFile             matchVariables      measureGeom         quit
    
25. relax               remove              restrainAngle       restrainBond
    
26. restrainTorsion     saveAmberParm       saveAmberParmNetcdf saveAmberParmPert
    
27. saveAmberParmPol    saveAmberParmPolPertsaveAmberPrep       saveMol2
    
28. saveMol3            saveOff             saveOffParm         savePdb
    
29. scaleCharges        select              sequence            set
    
30. set_default         setBox              showdefault         solvateBox
    
31. solvateCap          solvateDontClip     solvateOct          solvateShell
    
32. source              transform           translate           verbosity
    
33. zMatrix
    
34. 
    
35. For a list of the current aliases, type "alias".
    

复制代码

看你的log，明显是在loadpdb后报错的，自然应该检查下一句命令。我这里没装AmberTools25，用的AmberTools23，并没有removeH这个命令，可能是你报错的原因。