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