From: Josh Vermaas (
Date: Mon Jun 15 2015 - 15:03:16 CDT

Hi Louis,

The "MOLECULE DESTROYED" message is coming because of psfgen failing to
build a composite psf, not atomic positions of anything. The merge tool
reruns psfgen to regenerate the topological structure of your combined
system. What may be the case is that it can't find a topology file that
is referenced in your headers, causing psfgen to crash out when it
doesn't recognize a particular residue (probably your drug). The
alternative way of merging molecules together is with topotools
( At the very
bottom of the documentation, there is an example of the "mergemols"
command, which does not call psfgen again, but instead uses the atom
names, types, bonds, etc from the molecules already stored in VMD to
merge system pieces together. This will then get you a merged structure
which you can refine further to eliminate overlapping atoms.

-Josh Vermaas

On 6/15/15 1:24 PM, BALCZIAK, LOUIS wrote:
> Hello,
> I'm an undergrad research student working with VMD in order to test
> drug interaction with the human PGP-glycoprotein. Last summer, someone
> set up an equilibrated model of the protein. It is immersed in a lipid
> bilayer, and water molecules are added. I am very new to VMD, so
> trying to understand it fully has been daunting. I am trying to put a
> small drug into the model. I have the drug's PDB and PSF files. I also
> have all the necessary files for the protein and the topology files. I
> tried to merge the drug with the protein with the Merge tool. However
> it says the "MOLECULE DESTROYED" every time. I have tried dragging the
> drug to a spot with only water molecules and moving overlapping water
> molecules away to prevent failure to merge PDBs. Then I save the new
> pdb files for the drug's new position and the protein pdb due to the
> new coordinates for the water molecules. However, even when I do this
> the Merge tool still says that the molecule is destroyed. It fails to
> merge the files. Are there any Tcl console commands to help with this?
> Or is there a better method than dragging and dropping water molecules
> out of the way? Maybe deleting the water molecules that are within x
> Angstroms of the drug?
> Any feedback is very much appreciated,
> Louis Balcziak