AMBER Archive (2004)

Subject: Re: AMBER: restraining internal coordinates

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Thu Sep 16 2004 - 12:04:14 CDT

I'm not sure if dihedral angles are the best way to go, since a small
angle change
can propagate to a large motion at a distance.
however, if you want to try it, the sander dihedral angle restraints are
all listed with atom numbers, so each dihedral in the molecule can
have it's own target value. creating that set of restraints can be a big
pain,
and maybe the programs to do that will give the problem you described.
sander itself, though, has no problems keeping an arbitrary number of
dihedrals restrained to independent values.

if you really want to go this way and can't find another way,
my moil-view program can create a set of dihedral restraints
where the target values are extracted from a structure. you need to have
an SGI, though, and if you haven't used moil-view before there
may be easier ways to do it.
carlos

===================================================================
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
===================================================================

Taner E. Dirama wrote:

>Dear all,
>I would like to simulate a protein cluster consisting of 4 protein molecules in
>a solvent. I want to let the center of masses of the proteins move while to
>keep the internal coordinates of the proteins fixed (or restrained).
>ibelly and ntr options impose cartesion coordinate restraints which will keep
>the center of masses restrained as well. Torsional angle restraints in nmr
>options, as far as I understood from the manual, allows one to define the
>ranges of torsional angle values for specified dihedrals. However, same
>dihedral angles in the same type of residues in a protein may have
>significantly different dihedral angles. Therefore, the range specified would
>allow the proteins to deviate from their initial (crystalline) structures.
>
>Is there a way that can do this?
>
>Regards,
>
>
>
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