From: Abhishek TYAGI (atyagiaa_at_connect.ust.hk)
Date: Sun Nov 04 2018 - 06:33:55 CST
Hi,
to fix the atom, i.e. they will not move you can use the following script:
#Function: fix sheets
mol delete all
set input your-molecule
set output fixed-file
mol load psf $input.psf pdb $input.pdb
set all [atomselect top all]
$all set beta 0.0
set surf [atomselect top " Your selection "]
#$surf set resid 81
$surf set beta 1
$all writepdb $output.pdb
Thanks
Abhi
Abhishek Tyagi, PhD
Research Associate
Chemical and Biological Engineering
Hong Kong University of Science and Technology
Clear Water Bay, Hong Kong
________________________________
From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of Villalain Boullon, Jose <jvillalain_at_umh.es>
Sent: Sunday, November 4, 2018 5:18:23 PM
To: namd-l_at_ks.uiuc.edu
Cc: Villalain Boullon, Jose
Subject: namd-l: Fix aminoacids - error
Dear all,
I want to fix some amino acids (all the atoms in the residue) of a protein and for that I use the following script,
constraints on
consexp 2
consref 5iz.pdb
conskfile 5iz.fix
conskcol B
but, after some ns, I see that they are not fixed (they move).
Could you tell me what I am doing wrong.
Thanks a lot for your help ¡!.
José.
x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x
José Villalaín
Instituto de Biología Molecular y Celular - IBMC
Universidad "Miguel Hernández" - Campus de Elche
E-03202 Elche-Alicante (España-Spain)
x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x-x
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