RE: equilibrated the system

From: Luis Rosales (ludwig_at_biomedicas.unam.mx)
Date: Tue Jan 11 2005 - 17:49:16 CST

Hi Wuhan!!

Constraining atoms is simple and fun!! :P

constraints on #this is where you turn on the constraint
consRef rst.pdb #pdb file with the atomic coordinates used as reference
consKFile rst.pdb #pdb file with a column containing the constraining
values
consKCol B #column of the values used to constrain.

consKcol can be the x, y, z, O or B values columns (O for ocupancy, I guess)
this allows you to play with vmd to set different constrain values to
distinct parts of your system.
To constrain the CA trace of your protein, you open the pdb file that you
have choosen as the reference coordinates and type someting like this on the
vmd Tkconsole:

set all [atomselect top all]
set casel [atomselect top "protein and name CA"]
$all set beta 0
$casel set beta 0.75
$all writepdb rst.pdb

Voilá, you have now your constraint file!!!!
Notice that you can lower or turn off your constraints along your
simulation:

# Minimization
minimize 0
minimize 2500
reinitvels $temperature
run 500 ; #

constraintScaling 0.25
reinitvels $temperature
run 500 ; #

constraintScaling 0
reinitvels $temperature
run 500 ; #
minimize 500

Hope this helps.
Best regards,

Ludovico

> -----Mensaje original-----
> De: owner-namd-l_at_ks.uiuc.edu
> [mailto:owner-namd-l_at_ks.uiuc.edu] En nombre de Xiaoqing Wang
> Enviado el: Martes, 11 de Enero de 2005 08:43
> Para: NAMD
> Asunto: namd-l: equilibrated the system
>
> Hi all
>
> I have downloaded an example of an equilibration (or “restrained”) run
> input file(restrained_md_example.in) in web site
> http://mccammon.ucsd.edu/~rlaw/ctbp_workshop_rlaw.htm .
>
> #forcefield
...
> constraints on
> consref protein_only.coor
> conskfile protein_cons.pdb
> conskcol X
...
> #minimize 1000
> run 250000
>
> My question is how to prepare consref and conskfile files if I want to
> restrain protein?
>
> Thanks!!!
> --
> Wuhan University
> Wuhan
> China
>
>

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