From: Axel Kohlmeyer (
Date: Mon Jun 15 2015 - 14:49:29 CDT

On Mon, Jun 15, 2015 at 2:24 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

then this is something that you should be first and foremost
discussing with the person overseeing your project. it is near
impossible to teach somebody via e-mail.

> 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?

the merge tool uses the psfgen program as the backend and thus
requires a matching force field topology file, most likely your PDB
and PSF files are not commensurate with the one chosen. it looks to me
that you first should practice setting up simulations at all. there
are tutorials for that on the TCBG home page.
setting up a simulation with a protein immersed into a lipid bilayer
is a rather advanced procedure and it is practically impossible to get
this right without acquiring proper practical experience with all the
steps leading toward this.

again, you need to go over this with the person overseeing the
project. expecting that you can teach yourself all the necessary
skills all by yourself is unrealistic.


> Any feedback is very much appreciated,
> Louis Balcziak

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.