[AMBER] Adding single distance restraint

From: Adler, Marc <Marc.Adler.elan.com>
Date: Wed, 23 Dec 2009 19:00:35 -0700

Hello fellow AMBER users,


I am trying to include a single distance restraint in my MD simulations.


I am a new user of Amber and I am using SANDER for MD simulations. The
trajectories are analyzed to obtain information about protein/ligand
interactions. I am using a system setup by someone else and,
admittedly, I'm not sure what is going on.


All too often, the ligand leaves the binding pocket. I want to hold it
in place by using an NMR like distance restraint to define an H-bond.
My current input files (xxx.in) look like the edited file shown below
("..." refer to deleted sections). I want to include something in this
file that will restrain the distance between two atoms, specified by
atom number, to an upper bound of 4.0 ang.


--Minimize H of water only



imin=1,maxcyc=10000, ntmin=1, ncyc=1000, drms=0.1,

cut=999, ntb=0,




Restraint ligand


RES 243


Restraint residue 17


RES 17




-- Belly residues: ligand, site residues and water

RES 243 243


RES 192 192

RES 243 2006




Happy Holidays and a great New Year.


Marc Adler

Elan Pharmaceuticals


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Received on Wed Dec 23 2009 - 18:30:02 PST
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