AMBER/TLEAP如何按照想要的方法加氢

溪临昭煌

各位老师好，我想用AMBER对我的蛋白进行模拟，但是在使用tleap进行参数获取的时候发现程序总会按照自己的标准对我的体系进行处理和加氢，但是我想让某些残基按照我自己的设定进行加氢，便于后续分析，请问有办法实现吗？GMX里面可以在pdb2gmx部分实现这个功能，不知道AMBER是否有类似的方法？在此谢过各位老师了

rpestana94

Maybe you need to change the name of the residue, for example for histidine (HIS) amber has this notation:

HID: Histidine with hydrogen on the delta nitrogen

HIE: Histidine with hydrogen on the epsilon nitrogen

HIP: Histidine with hydrogens on both nitrogens; this is positively charged.

I don't know if this is what you are looking for

溪临昭煌

rpestana94 发表于 2023-7-18 21:31
Maybe you need to change the name of the residue, for example for histidine (HIS) amber has this not ...

Thanks for your kind suggestion. I will try it later.