RE: Targeted and Steered MD: Why must the initial and targeted PDBs have identical # of atoms?

From: Tristan Croll (
Date: Tue Aug 27 2013 - 19:27:26 CDT

Hi Bryan,

The best way to handle this is to take your protein in its starting configuration, set your TMD atoms to their target configuration (and set their occupancy, beta etc.) and then write this as your target file. It will typically look incredibly ugly - but this doesn't matter, because NAMD is only interested in the positions of the flagged atoms. To do this, load your starting structure and the pre-existing target structure and then use something like:

set all [atomselect *starting structure MOLID* all]
$all set beta 0
$all set occupancy 0
set target [atomselect *target MOLID* "*target atoms*"]
set tomove [atomselect *starting structure MOLID* "*target atoms*"]
$tomove set {x y z} [$target get {x y z}]
$tomove set occupancy 1
$all writepdb target.pdb



From: [] On Behalf Of Bryan Roessler
Sent: Tuesday, 27 August 2013 2:25 AM
Subject: namd-l: Targeted and Steered MD: Why must the initial and targeted PDBs have identical # of atoms?

This is a limitation that has been hindering me for some time. Running targeted or steered MD on a protein in explicit solvent is quite difficult because both the initial and targeted PDBs must contain the same number of atoms. When the protein is in different conformations, random distribution of solvent usually results in a different number of atoms between the two systems, causing NAMD to complain, even though I am only targeting atoms within the protein. I have been manually removing water molecules from the corners of the solvation box in order for the numbers to match but this can still be problematic due to having to regenerate the PSF. Is there an easy workaround for this? Could TMD and SMD in NAMD be implemented such that only atoms selected for targeting using occupancy values are considered in the comparison?


Bryan Roessler | Graduate Research Assistant
UAB | The University of Alabama at Birmingham<>
Knowledge that will change your world

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