From: Dallas Warren (
Date: Tue May 15 2018 - 20:23:27 CDT

Can't help with the first 1/ 2/, however with 3/ vmd generates bonds
to display based on the distance that the molecules are apart, not due
to any bonds present within a topology.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
When the only tool you own is a hammer, every problem begins to resemble a nail.

On 16 May 2018 at 07:59, fan li <> wrote:
> Hi every one
> I have molecule1 in the middle of my box, and molecule2 at the bottom. Now I
> want to fill the other volume not occupied by molecule1 and molecule2. I
> tried following command
> solvate ubq.psf ubq.pdb -t 5 -o ubq_wb
> It created the water around the molecule1 and molecule2, but the molecule2
> is already at the boundary of my box,so there should be no waters below it.
> (1)How can I fill the other volume not occupied by molecule1 and molecule2
> in vmd?
> (2)And what is the density of the solvate?
> (3)I also noticed that my original psf might be changed after I used the
> solvate ubq.psf ubq.pdb -t 5 -o ubq_wb because some non-physical bonds is
> generated in the display window? Why it happend?
> Fan