From: Joao Ribeiro (
Date: Tue Jun 18 2019 - 09:38:50 CDT

Dear Alex,


This message belongs to and not vmd-l.


In fact, the pdb containing the declaration of the atoms to be kept fixed and the pdb used to run the simulations have to have exactly the same atoms.


Did you prepare the “fixed_coordinates” from the pdb that you used to run the simulation? In this case, you can use VMD to load you initial psf and pdb, and then execute the following commands.


set selAll [atomselect top “all”]

set selFixed [atomselect top “index x to y”]


$selAll set occupancy 0.0; # set the occupancy of all atoms to 0.0

$selFixed set occupancy 1.0; # set the occupancy of selected atoms to 1.0


$selAll writepdb fixed_coordinates.pdb; #export the pdb


I hope this helps






João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois

+1 (217) 3005851


From: <> on behalf of Alessandro Ruda <>
Date: Monday, June 17, 2019 at 5:13 PM
To: "" <>
Subject: vmd-l: Error during minimizazion - Number of atoms in fixed atoms PDB...




I'm running a minimization on a protein with fixed coordinates. I get the not certainly original fatal error:


Number of atoms in fixed atoms PDB doesn't match coordinate PDB.


I basically copy-pasted the coordinates from the original .pdb file for the simulation in the 'fixed_coordinates' file, still getting the same error.

The occupancy is already set to 1.00 and now I'm stuck with this error.

Does anyone have a hint on this?


Thank you,