[AMBER] restraintmask: select residues around the coordinates of a point

From: Thomas Evangelidis <tevang3.gmail.com>
Date: Mon, 25 Jul 2016 01:51:43 +0200



I would like to do equilibration of the structures of many proteins without
their ligands, but to keep flexible only the residues within the binding
pocket. For this purpose I must write a restraint mask, but when I find the
pocket residues using "ambmask"​, the resulting ""maskstr" exceeds the
limit of 80 characters. The other alternative I could think would be to
form the protein-ligand complex, find the coordinates of the COM of the
ligand, and then simulate the protein alone using restraintmask="! (
([coordinates] <: 5) )". However, I am not sure if this is possible. Any
ideas about possible solutions would be greatly appreciated.

thank you in advance for any suggestions,

Thomas Evangelidis
Research Specialist
CEITEC - Central European Institute of Technology
Masaryk University
Kamenice 5/A35/1S081,
62500 Brno, Czech Republic
email: tevang.pharm.uoa.gr
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Sun Jul 24 2016 - 17:00:02 PDT
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