Sorry to forget to point out that MG1, MG2, MG3 are ligands name.
Ning
-------- Forwarding messages --------
From: "ning via AMBER" <amber.ambermd.org>
Date: 2025-04-15 19:09:45
To: "amber maillist" <amber.ambermd.org>
Subject: [AMBER] Request help: how manipulate the prmtop file to add exclusion force
Hi Amber experts,
I hope this email find you going well. Recently, I tried to simulate a protein receptor with multiple ligands in water system by using Amber24. However, these ligands can aggregate together due to they own a little hydrophobicities. So, I would like to add a external force to push away them each other, or emliminate themselves some kind of interactions, meanwhile keep the interaction with receptor protein. I think that way maybe provide an equal opportinuty for each ligands to bind with receptor.
Acutually, I had tried to modify the prmtop file by the addExclusions function in ParmED software, like this:
parm com.prmtop
addExclusions :MG1 :MG2
addExclusions :MG2 :MG3
addExclusions :MG1 :MG3
outparm com_exclu.prmtop
Then, it give me a new topology file named com_exclu.prmtop. But, in real simualtion case (I used ff19SB for protein, gaff for ligands, and OPC for water molecules.), this action doesn't work. These ligands still aggregate with each other. So how do I manipulate this topology file to reach this goal. Please help me! Thanks so much for any suggestions.
Best,
Ning
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Received on Tue Apr 15 2025 - 04:30:02 PDT
