Re: AMBER: Restraint of atoms during minimization

From: Carlos Simmerling <>
Date: Tue, 22 Feb 2005 11:34:06 -0500

1) you're using Cartesian coordinate restraints to restrain a dihedral
why not just use dihedral angle restraints? check the sander manual for

2) if you want to keep using the Cartesian restraints,
you might need a strong force constant than 1.0 to keep the atoms from
moving, try using 10 or 50 and see if that helps.

Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web:
Stony Brook, NY 11794-5115 E-mail:

L Jin wrote:

>Dear AMBER users,
>I am using AMBER7 and trying to run restraint minimization with the following
>input file so that I can fix the five atoms which defined two dihedral angles.
>I used the initial structure coordinate file as the reference for the
>restraint. But when I checked the ouput structure, the dihedral angles, which
>are supposed to be fixed, actually changed. Did I do something wrong or not
>successfully define the restraint? Could anybody give me some suggestions? Many
>thanks in advance.
>Minimization with sander (Amber7)
> &cntrl
> imin = 1, maxcyc = 50000, drms = 0.0005, ntb = 0,
> ntpr = 100, cut = 999., ncyc = 1000, ntr=1,
> &end
>Group input for restrained atoms of dihedral angles
> 1.0
>ATOM 28 32
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Received on Tue Feb 22 2005 - 16:53:02 PST
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