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

[Miao, Y. <Yin...@me...>]

Hi Yuxuan,

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.

We had LiGaMD3 originally coded in Amber22, but it’s officially released only in Amber24+. So the best may be to use Amber24, which is free to academia anyway.


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?

PPI indicates that the two protein binding partners are not covalently connected, and PPI-GaMD is implemented as such.
In your case, Pep-GaMD might be a better approach to examine domain motions in one protein as the region you select (defined in “ timask1/scmask1”) could be covalently connected to other parts of the protein.

Best,
Yinglong


Yinglong Miao, Ph.D.
Associate Professor
Department of Pharmacology and
Computational Medicine Program
University of North Carolina - Chapel Hill
Tel: 1-919-962-5696
http://miaolab.org<http://miaolab.org/>

Editor-in-Chief
npj Drug Discovery
https://www.nature.com/npjdrugdiscov

On Oct 29, 2025, at 12:28 AM, 王宇轩 <sjt...@sj...> wrote:

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


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