VMD-L Mailing List

From: Paul Grayson (pgrayson_at_ks.uiuc.edu)
Date: Wed Apr 03 2002 - 14:05:41 CST

> Why does not VMD determine bonds for every structure file?

VMD just has one set of bonds for each Molecule loaded. For
animations, just the coordinates are updated at each step - the bonds
remain the same. We are looking into ways to make this more flexible,
since more and more people would like to be able to change bonds
during an animation.

> I know that my pdb files have many ideltical water molecules but that is

Why do you need multiple identical water molecules? Remove the
duplicates, and it will be draw correctly.

> If VMD use the criterion distance to make the bonds for each pdb
> file then there will be no problem, isn't it?

VMD's distance-based search expects a structure that makes physical
sense. In your case, VMD tries to draw bonds between any two
identical atoms, and to each copy of the atoms they are supposed to be
bonded to. You will therefore get three bonds connected to each H
atom, and four to each O. There is no way VMD can separate two water
molecules with identical coordinates!

If you really want VMD to handle your pdb files, you will need to make
a psf file that specifies the bonds you want. VMD can't possibly
guess them correctly.

-Paul