From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Oct 18 2009 - 09:25:30 CDT

On Tue, Oct 13, 2009 at 5:54 PM, Peter Murphy <murffyp_at_gmail.com> wrote:
> Hello everyone,

hello peter,

as you may have concluded, there is something wrong with your request for
help, but posting the same question to a different mailing list is only going
to increase you chances marginally. the most important step is that you
have to make it easy to reproduce what you are seeing, and here you are
very vague. i'm adding some comments below.

> I have used the solvation script before without problem, but now what I am

_which_ solvation script? taken from where??

> trying to use it on a different PDB/PSF set, things are going wacky. First,
> I am getting a water box instead of a water sphere. Secondly, instead of the

what is the input, what are the settings you are using?

> water being centered around my protein of interest, the corner of the box
> starts at the center of my protein, resulting in only 1/4 of the protein
> being solvated, and a HUGE water box (8 - 9 times the volume of my protein).
> Any suggestions?? (I have the output PDB/PSF available if it helps!)

have you tried this with a simple/smaller system?

it would be best if you can provide an exact protocol how to get
to the same result that you are getting. the output is not very
helpful. your problem has to lie in how you get there.

cheers,
   axel.

>
> Thanks in advance!
>
> Peter
>
>

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.