Hi, Kress!
Not really.
Usually, small molecules tend to aggregate together to form a ball-like structure, and I want to prevent it in my simulation!
One method is to applied repulsive forces between Virtual Interaction Sites (VIS) which are placed evenly all over the molecule.
The repulsive force is formulated through the reassignment of the Lennard-Jones’ parameters.
I am thinking of another possibility. Like the idea of a parallel universe, where I can put the ligands together in a single system , however, they have no non-bond interactions, so that they would not aggregate together.
I don't know if there are some "masks" to specifically disable the non-bond interaction only between the ligands without the impact on the interactions between the ligands and the protein.
Thanks for your reply!
Pineapple
发件人: "James Kress" <jimkress_58.kressworks.org>
收件人: "amber" <amber.ambermd.org>
发送时间: 星期六, 2021年 4 月 24日 上午 3:00:52
主题: Re: [AMBER] Make the two ligands independent in one simulation
So, are you trying to modify the laws of Physics to prevent the simulation
from providing physically accurate results?
James Kress Ph.D., President
The KressWorks(r) Institute
An IRS Approved 501 (c)(3) Charitable, Nonprofit Corporation
“ENGINEERING THE CURE” (c)
(248) 573-5499
Learn More and Donate At:
Website: http://www.kressworks.org
Confidentiality Notice | This e-mail message, including any attachments, is
for the sole use of the intended recipient(s) and may contain confidential
or proprietary information. Any unauthorized review, use, disclosure or
distribution is prohibited. If you are not the intended recipient,
immediately contact the sender by reply e-mail and destroy all copies of the
original message.
-----Original Message-----
From: 李明玉 <santaclaus.sjtu.edu.cn>
Sent: Friday, April 23, 2021 10:19 AM
To: amber <amber.ambermd.org>
Subject: [AMBER] Make the two ligands independent in one simulation
Hi, Amber users
Thanks for your attention!
I would like to study two ligands binding behavior in one protein system
simultaneously in a single MD trajectory.
However, the ligands prefer to aggregate together due to the polarity.
I am wondering is there any possible way to make those two ligands
independent in a single MD trajectory.
In other words, there is no non-bond energy between the two ligands, so that
they can move independently though they are in one protein system!
Many thanks
Pineapple
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 23 2021 - 20:00:02 PDT
