[GaMD-discuss] Some questions about LiGaMD3 and PPI-GaMD

[王宇轩 <sjt...@sj...>]

Dear Sir/Madam,

I want to use LiGaMD3 and PPI-GaMD in Amber22/23 suites,but now have some questions about the application scop of them.

Question 1: Is LiGaMD3 available in Amber22/23 ?

I have read the article about the devalopment of LiGaMD3(J. Chem. Theory Comput. 2024, 20, 14, 5829-5841), 
and Amber23 is referred to as the simulation tool in this article.
However, I find no description about the parameter "igamd=28" that applies triple boost on the ligand in Amber 2023 mannual,
and thus I'm not sure if LiGaMD3 available in Amber22/23.


Question 2: Could PPI-GaMD be applied to simulation of the interactions between protein domains in the same protein?

One of the protein systems of my interest experience large conformation change during activation, 
and one damain in it will rotate away from others in the same protein.
As the internal interactions between domains are similar to PPI in my viewpoint,
I wonder whether PPI-GaMD could be used to study the dissociation of one domain from the others, 
or GaMD is a better choice?


Any suggestions from you would be highly appreciated.
Thanks in advance.


With best regards, 
Yuxuan Wang

School of Pharmaceutical Sciences，
Shanghai Jiao Tong University