AMBER Archive (2005)

Subject: Re: AMBER: Restraint of atoms during minimization

From: L Jin (s0344557_at_sms.ed.ac.uk)
Date: Tue Feb 22 2005 - 11:12:13 CST

Thank you very much for reply.

It seems to me that the makeCHIR_RST command is used to generate dihedral
restraint for amino acids only. But my molecule is a disaccharide. And I want
to fix the two dihedral angles across the glycosidic linkages.

When I used the makeCHIR_RST and a pdb input file, it returned nothing in the
output file. So I turned to use the Cartesian coordinate restraints. I tried 50
just now but still not restrain the atoms moving.

Is there any other method to do this kind of minimization with restraint of
dihedral angles for saccharide within AMBER? By the way, is it reasonable to
use
Cartesian coordinate restraints to restrain a dihedral angle?

Many thanks.

Quoting Carlos Simmerling <carlos_at_ilion.bio.sunysb.edu>:

> 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_at_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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