VMD-L Mailing List

From: BALCZIAK, LOUIS (lkbalcziak_at_coe.edu)
Date: Mon Jun 15 2015 - 13:24:49 CDT

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