[gmx-users] steered pulling code on ligand-receptor complex

Jianguo Li ljggmx at yahoo.com.sg
Wed Oct 31 09:21:49 CET 2012

If you position restraint the receptor or only use several residues at the binding site, in both cases you limit your sampling to a small part of the phase space and the PMF may not be accurate, since the receptor may undergo conformational change upon ligand binding.

----- Original Message -----
From: 范聪 <fanc232 at nenu.edu.cn>
To: gmx-users at gromacs.org
Sent: Tuesday, 30 October 2012, 20:04
Subject: [gmx-users] steered pulling code on ligand-receptor complex

Hello, everyone!
    I'm a new user in gromacs, and now I have to perform a steered pulling code on a ligand-receptor complex. The ligand is to be pulled away from the binding site of the receptor, and umbrella sampling will be used to gain the PMF (potential mean force) curve. Then  binding energy of the ligand-receptor complex would be estimated.  The receptor contains 303 residues. While the ligand is pulling away, the whole receptor is restrained by posres, 1000 in x, y and z axis.
   Since the receptor is so large and umbrella sampling needs so much calculations, a very long time will be taken to complete the work.
   Now I have my question, is there anyway to reduce the taken time? Such as keeping only residues near the binding site to respect the whole receptor?
   Thank you all in advance!

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