From: Richard Wood (
Date: Wed Jul 27 2016 - 14:17:39 CDT

Couldn't one create a water box that is the correct dimensions that they need? I know this is easy to do in CHARMm. I might even have a script to create a box starting with a 24.xxxx per side box of 512 waters.

From: [] on behalf of Amy Rice []
Sent: Wednesday, July 27, 2016 12:46 PM
To: vmd-l
Subject: Re: vmd-l: Custom Water Box

Hi Jack,
I believe the issue is that when you add water molecules the second time, they are being given the same segment name prefix as the first round of solvation. I'm not sure how to change the prefix in the solvate plugin text inferface, but the GUI has an option to change the prefix, which fixes this problem in my experience.

Hope this helps,
- Amy

On Tue, Jul 26, 2016 at 7:13 PM, Jackson Cavett <<>> wrote:
I have been trying to use this method, but again ran into the problem. I tried a few different things, and think I narrowed down the problem. First, I created a waterbox around the original molecule PDB file (with no water) and then added more water molecules. This worked perfectly. However, when I tried to add water molecules to the PDB file in which the waterbox is already included, I got the error:

duplicate segment key WT1
ERROR: failed on segment
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.

No matter what the coordinates of the new waterbox, the error occurs. So I believe it is an issue in which I am trying to solvate something that has already been solvated. Is there a different way to add water molecules to the PDB file when it starts in a waterbox?

Thanks Again,


On Mon, Jul 25, 2016 at 10:00 PM, James Kress <<>> wrote:
Can’t you just specify minmax so that min is the largest (in magnitude) -Z you want and max is a Z value at the minimum Z border of your existing box?


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From:<> [<>] On Behalf Of Jackson Cavett
Sent: Monday, July 25, 2016 9:35 PM
To: vmd-l <<>>
Subject: vmd-l: Custom Water Box

Hello All,

I am currently equilibrating the integrin áVâ3 in a waterbox using NAMD. When it is done, I would like to add some water molecules to it, but only in the -z direction. Currently, the áVâ3 pdb and psf files have a waterbox in which I used the following in the Tk Console (from the NAMD tutorial):

solvate myfile.psf myfile.pdb -t 5 -o myfile_waterbox

I just tried using this in the Tk Console to create my new waterbox:

package require solvate
solvate myfile.psf myfile.pdb -minmax {{-X -Y -Z} {X Y Z}} -o myfile_watercube

with my custom waterbox dimensions, but I can't use this method when a waterbox already exists because it creates duplicate, overlapping water molecules. Is there a way to add water molecules a certain distance in only one direction? Any help would be greatly appreciated!

Thank You,


Amy Rice
Ph.D. Student
Physics Department
Illinois Institute of Technology