[AMBER] How to deal with the metal center contain a phosphorylated amino acid by MCPB.py

Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

From: 吕思凡 via AMBER <amber.ambermd.org>
Date: Thu, 6 Jul 2023 09:54:15 +0000

Hi,

I’m trying to build a complex contain metal MG, ligand, a phosphorylated amino acid. The phosphorylated amino acid require binding to MG.

but I don’t know how to deal with the phosphorylated amino acid from this tutorial MCPB.py(https://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.php).

I need to prepare mol2 file and frcmod file for the phosphorylated amino acid, and to set the MCPB.in file such tutorial 1OKL.in.

Please help me to solve this problem.

Best,
Sifan lyu

AlloStar Platform, Nutshell Therapeutics

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jul 06 2023 - 03:00:02 PDT