[AMBER] Restraining ligand for TI

From: Delwakkada Liyanage, Senal Dinuka <sdd313.msstate.edu>
Date: Tue, 19 Oct 2021 22:34:13 +0000

Hello everyone,

I am simulating a ligand decoupling from a DNA system and my ligand leaves the binding area at the furthest lambda values. I have already run a decharging step and this happen at the vdW decoupling step. I understand I must implement a restrain to avoid this. I have two questions concerning this.

  1. What kind of restraining do you normally use? NMR restrains (&rst - nmropt =1) or position restrains (&cntrl - ntr=1)?
  2. Secondly, should I run a separate leg for all the lambda windows with the restraint?

Ps. I'm using pmemd and pmemd.cuda version 16

I appreciate your valuable feedback.


Senal Liyanage
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Received on Tue Oct 19 2021 - 16:00:02 PDT
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