哇卡卡卡卡卡 发表于 2022-9-23 20:39
好的，老师！也就是我先单独建一个二氯甲烷的溶剂盒子，对应的产生frcmod文件和mol2文件。但是不知道后面 ...

the pdb of the system that you load into leap needs to be the one with the substrate already in it, you can't (as far I know) try to use the solvate function from leap with your own solvent.

So put your substrate in the dichloromethane, you can use packmol to generate this pdb, and in leap upload the dichloromethane parameters, the substrate parameters and then upload the pdn of the whole system (substrate + dichloromethane)

rpestana94 发表于 2022-9-23 23:34
You need the parameters for the dichloromethane, the frcmod and the prep file, and the dichlorometha ...

好的，老师！也就是我先单独建一个二氯甲烷的溶剂盒子，对应的产生frcmod文件和mol2文件。但是不知道后面怎么将底物载入盒子里。我只知道水盒子就直接用tleap直接载入，水盒子是amber自带的，不知道自己建立的溶剂盒子怎么操作

You need the parameters for the dichloromethane, the frcmod and the prep file, and the dichloromethane alone as pdb or mol2, with that you can load your system with the box constructed with dichloromethane, with that in leap you can get the prmtop and inpcrd files for your system.