From: Marcos Sotomayor (sotomayo_at_ks.uiuc.edu)
Date: Sat Mar 25 2006 - 16:36:28 CST
It may be easier to use tcl forces to add an harmonic constraint to a
particular dihedral. Look at the NAMD user's guide:
At the end of the section "Tcl Forces and Analysis" there is a script that
does that (Be careful with IDs of atoms, as NAMD labels them
starting from 1 and VMD starting from 0).
Otherwise, you would need to modify your psf file and parameter file (see
detailed descriptions of both at the end of the NAMD tutorial,
On Sat, 25 Mar 2006, xiaojing gong wrote:
> Thank you for your advice, if I want to constrain the dihedral
CB--CG--CD--NE of Arg residue. Do I need to define a new bond ? would
you give me more details about the technique . I am a fresh man in this
field, I really need someone to give me more details.
> "Leonardo G. Trabuco" <ltrabuco_at_ks.uiuc.edu> Ð´µÀ£º
> On Fri, Mar 24, 2006 at 08:55:34AM +0800, xiaojing gong wrote:
>> I want to constrain a dihedral angle so that it can maintain
>> a constant value during the simulation, BUT I don't konw how
>> to do that? Could anyone help me?
> You could alter the parameter file, setting a high force constant for
> the desired dihedral. In the likely case that this would affect other
> dihedrals that you don't want to constrain, you would have define new
> some new atom types.
> Leonardo Giantini Trabuco
> Ph.D. student
> Center for Biophysics and Computational Biology
> University of Illinois at Urbana-Champaign
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