VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Thu Dec 11 2014 - 15:05:14 CST

Hey,

I am not sure what is going on with the script that you are using. If its
the same size as the protein I guess its safe to say that you are not
plugging in the correct radius.

I use a cubic box - here is my code:

set bb [list "$x_min" "$y_min" "$z_min"]
set cc [list "$x_max" "$y_max" "$z_max"]
set minmax2 [list "$bb" "$cc"]

#SOLVATE
package require solvate
solvate input_1.psf input_2.pdb -minmax $minmax2 -o output_2_0

before this I use measure minmax to get 6 numbers returned - in two rows of
the list - one have minx, miny & minz and the other having maxx, maxy and
maxz. These are dimensions of the bounding box that can hold your protein.
I then seperate those and each dimension is padded (I pad by 15A in each
dimension ~ since I use a cutoff of 12A and 14A for my switching function)
and pass the new min - max to the code above.

The above creates output_2_0.pdb and output_2_0.psf.

Hope this helps,

Best,
/A

On Fri, Dec 12, 2014 at 4:53 AM, Kshatresh Dutta Dubey <kshatresh_at_gmail.com>
wrote:

> Dear Users,
>
> I want to add the solvation shell around the 10 A form the protein
> exterior. Is there any script to do so?When I am using the
> wat_spherical.tcl of tutorial, it is just adding the water sphere of almost
> radius of the protein and also waters have the different segement ids from
> WT1 to WT8. Please suggest me a proper way to add solvation shell.
> I will be thankful for all suggestions.
> Thanks in advance
>
> Regards
> Kshatresh
> 

-- 
Best,
/A