Re: Fix aminoacids - error

From: Abhishek TYAGI (
Date: Sun Nov 04 2018 - 06:33:55 CST


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



Abhishek Tyagi, PhD
Research Associate
Chemical and Biological Engineering
Hong Kong University of Science and Technology
Clear Water Bay, Hong Kong

From: <> on behalf of Villalain Boullon, Jose <>
Sent: Sunday, November 4, 2018 5:18:23 PM
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 Villalaín

Instituto de Biología Molecular y Celular - IBMC

Universidad "Miguel Hernández" - Campus de Elche

E-03202 Elche-Alicante (España-Spain)


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