Hi Ning,
Have you tried the rst feature in cpptraj?
https://amberhub.chpc.utah.edu/rst/ . You may also find it on page 712 of the AMBER24 use manual.
After doing what this tutorial said, you will be able to apply NMR restraints to the ligands by making the end of your MD input look like this (assuming you are using pmemd).
...<other MD inputs like nstlim, ntpr, etc.,>...
nmropt=1,
/
&wt type='END'
/
DISANG=output
/
&ewald
nfft1=48, nfft2=48, nfft3=48,
/
Wish all the best!
_____________________
Zhen Li<
http://lizhen62017.wixsite.com/home>, Ph.D.,
The Merz Research Group<
http://merzgroup.org>,
Michigan State University,
Cleveland Clinic.
________________________________
From: ning via AMBER <amber.ambermd.org>
Sent: Tuesday, April 15, 2025 7:13 AM
To: amber maillist <amber.ambermd.org>
Subject: [AMBER] Fw: Request help: how manipulate the prmtop file to add exclusion force
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 - 05:30:02 PDT
