AMBER Archive (2009)

Subject: [AMBER] Adding single distance restraint

From: Adler, Marc (Marc.Adler_at_elan.com)
Date: Wed Dec 23 2009 - 20:00:35 CST

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

&cntrl

ibelly=1,

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

cut=999, ntb=0,

ntpr=500,

ntr=1,

/

Restraint ligand

10.0

RES 243

END

Restraint residue 17

10.0

RES 17

END

...

END

-- Belly residues: ligand, site residues and water

RES 243 243

...

RES 192 192

RES 243 2006

END

END

 

Happy Holidays and a great New Year.

 

Marc Adler

Elan Pharmaceuticals

 

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