VMD-L Mailing List

From: Jackson Cavett (jcavett_at_mail.bradley.edu)
Date: Tue Jul 26 2016 - 19:13:32 CDT

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,

Jack

On Mon, Jul 25, 2016 at 10:00 PM, James Kress <jimkress_58_at_kressworks.org>
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?
>
>
>
> Jim
>
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> *From:* owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] *On
> Behalf Of *Jackson Cavett
> *Sent:* Monday, July 25, 2016 9:35 PM
> *To:* vmd-l <vmd-l_at_ks.uiuc.edu>
> *Subject:* vmd-l: Custom Water Box
>
>
>
> Hello All,
>
>
> I am currently equilibrating the integrin αVβ3 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 αVβ3 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,
>
>
>
> Jack
>
>
>