VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Wed Jul 27 2016 - 15:08:29 CDT

Hi Jack,

Change the default segname. Psfgen doesn’t let segnames clash, and will bail out. Usually, when I put waters on either side of a membrane, the first segment use WT, and the second set of segments uses WA. Lookup the exact syntax on how to do this in the solvate plugin documentation online.

Josh Vermaas

Director’s Postdoctoral Fellow
National Renewable Energy Laboratory
joshua.vermaas_at_nrel.gov<mailto:joshua.vermaas_at_nrel.gov>

On Jul 26, 2016, at 6:13 PM, Jackson Cavett <jcavett_at_mail.bradley.edu<mailto:jcavett_at_mail.bradley.edu>> 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,

Jack

On Mon, Jul 25, 2016 at 10:00 PM, James Kress <jimkress_58_at_kressworks.org<mailto: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> [mailto: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<mailto: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