Hello,
This is ideally suited for nmropt=1. This is described in fair detail
in the Amber manual. ibelly fixes the absolute location of atoms, and
ntr applies a harmonic restraint to a reference structure that has a
fixed location in cartesian space.
What you're trying to do here sounds like adding a biasing potential
to a single degree of freedom while leaving the rest more or less
untouched (to the extent that this distance is decoupled from those
other degrees of freedom). ibelly and ntr do not succeed in this
regard, but nmropt does.
Take care to pay attention to the flat-well potential form so that you
choose k1, k2, r1, r2, r3, and r4 to obtain the behavior that you
want.
Good luck!
Jason
On Wed, Dec 23, 2009 at 9:00 PM, Adler, Marc <Marc.Adler.elan.com> wrote:
> 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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--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Dec 23 2009 - 19:30:03 PST
