VMD-L Mailing List

From: Amy Rice (arice3_at_hawk.iit.edu)
Date: Wed Jul 27 2016 - 12:46:51 CDT

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 <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>
> 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
>>
>>
>>
>
> 

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