Re: Re Re: how to constrain a dihedralqangle=3F?=

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:

http://www.ks.uiuc.edu/Research/namd/2.6b1/ug/node32.html#SECTION00096700000000000000

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,
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/index.html
)

Marcos

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.
> GXJ
>
> "Leonardo G. Trabuco" <ltrabuco_at_ks.uiuc.edu> д
> 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.
>
> Leo
>
> --
> Leonardo Giantini Trabuco
> Ph.D. student
> Center for Biophysics and Computational Biology
> University of Illinois at Urbana-Champaign
>
>
>
> ---------------------------------
> Ż1Gٷְٷ
> Ż-ɱɧ

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