Re: TMD: initial and targeted structure does not have same number of atoms

From: Jeff Comer (
Date: Tue Mar 07 2017 - 10:15:39 CST

What you need is to copy the coordinates from the target structure to
the simulation structure to produce a new structure with the same
atoms as the simulation structure but with the protein positioned as
in the target. You can do this with VMD:

mol new target_struct.pdb
set s0 [atomselect top "protein and name CA"]

mol new sim_struct.psf
mol addfile sim_struct_init.pdb
set s1 [atomselect top "protein and name CA"]

# Check that your selections have the same number of atoms.
puts "[$s0 num] [$s1 num]"
# Copy the coordinates
$s1 set {x y z} [$s0 get {x y z}]

# Write the result.
set all [atomselect top all]
$all writepdb sim_struct_target.pdb

Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311

On Tue, Mar 7, 2017 at 9:42 AM, Rabeta Yeasmin <> wrote:
> Hi,
> I am trying to set up a TMD simulation of a protein-lipid system. In the
> targeted structure, the protein is inside the lipid while protein is outside
> the lipid in the initial structure. I have tried to set up initial structure
> using charmm-gui (the program used to set up the targeted structure). But it
> looks like the total number of atoms is different in the targeted and
> initial(charmm-gui) structure. It may due to different number of water
> molecules in the two structure.
> How can I set up the initial structure having same number of molecules as
> the targeted structure?
> Can anyone please help me with this?
> Thank you.
> Rabeta Yeasmin

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