1) you're using Cartesian coordinate restraints to restrain a dihedral
angle-
why not just use dihedral angle restraints? check the sander manual for
details
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: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling.stonybrook.edu
===================================================================
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
>END
>END
>
>
>Lan
>
>
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Received on Tue Feb 22 2005 - 16:53:02 PST
