求助：用MCPB建模得到tleap.in文件，里面默认是水盒子，怎么把溶剂水换成二氯甲烷？

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我现在已经用MCPB对金属有机化学成功建模，生成了对应的tleap.in文件，但是里面默认是水盒子，怎么把溶剂水换成二氯甲烷呢，我现在有二氯甲烷的mol2文件、frcmod文件和lib文件，进行如下修改：source leaprc.protein.ff19SB
source leaprc.gaff
SUS = loadmol2 DCM-smd.mol2
saveoff SUS DCM-smd.lib
loadoff DCM-smd.lib
addAtomTypes {
        { "M1"  "Fe" "sp3" }
        { "Y1"  "N" "sp3" }
        { "Y2"  "N" "sp3" }
        { "Y3"  "N" "sp3" }
        { "Y4"  "N" "sp3" }
        { "Y5"  "Cl" "sp3" }
        { "Y6"  "O" "sp3" }
}
FE1 = loadmol2 FE1.mol2
ML1 = loadmol2 ML1.mol2
loadamberparams MOL.frcmod
loadamberparams frcmod.ions1lm_126_tip3p
loadamberparams TSb2_mcpbpy.frcmod
mol = loadpdb TSb2_mcpbpy.pdb
bond mol.1.FE mol.2.N1
bond mol.1.FE mol.2.N2
bond mol.1.FE mol.2.N3
bond mol.1.FE mol.2.N4
bond mol.1.FE mol.2.Cl1
bond mol.1.FE mol.2.O
savepdb mol TSb2_dry.pdb
saveamberparm mol TSb2_dry.prmtop TSb2_dry.inpcrd
solvatebox mol SUS 25
addions mol Na+ 0
addions mol Cl- 0
savepdb mol TSb2_solv.pdb
saveamberparm mol TSb2_solv.prmtop TSb2_solv.inpcrd
quit
出现错误：  
/public/software/apps/amber20/bin/teLeap: Fatal Error!
addIons: Argument #2 is type String must be of type: [unit]

    addIons unit ion1 #ion1 [ion2 #ion2]
      UNIT                      _unit_
      UNIT                      _ion1_
      NUMBER                    _#ion1_
      UNIT                      _ion2_
      NUMBER                    _#ion2_
Adds counterions in a shell around _unit_ using a Coulombic potential
on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be
opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise,
the specified numbers of _ion1_ [_ion2_] are added [in alternating order].
If solvent is present, it is ignored in the charge and steric calculations,
and if an ion has a steric conflict with a solvent molecule, the ion is
moved to the center of said molecule, and the latter is deleted. (To
avoid this behavior, either solvate _after_ addIons, or use addIons2.)
Ions must be monoatomic. Note that the one-at-a-time procedure is not
guaranteed to globally minimize the electrostatic energy. When neutralizing
regular-backbone nucleic acids, the first cations will generally be added
between phosphates, leaving the final two ions to be placed somewhere around
the middle of the molecule.
The default grid resolution is 1 Angstrom, extending from an inner radius
of (max ion size + max solute atom size) to an outer radius 4 Angstroms
beyond. A distance-dependent dielectric is used for speed.



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

求指导！

Frozen-Penguin

这个错误是因为你没有完整加载包含NA和CL离子的力场参数，而不是溶剂种类的问题。随便加载一个水模型，例如source leaprc.water.opc，然后输入list看看，如果显示有Na+Cl-就可以加离子了。

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Frozen-Penguin 发表于 2022-10-8 00:17
这个错误是因为你没有完整加载包含NA和CL离子的力场参数，而不是溶剂种类的问题。随便加载一个水模型，例如 ...

非常感谢，我以为那是溶剂水的力场参数就把它给删掉了