VMD-L Mailing List

From: Thomas C. Bishop (bishop_at_latech.edu)
Date: Wed Jun 27 2012 - 08:24:30 CDT

And here's a VMD script I useto randomly pick waters from a system and
replace them with salt. (Na Cl atoms or whatever you like)

http://dna.engr.latech.edu/~bishop/VMD/DashofSalt.v2.vmd

I think it's farily well commented and tested.

The script
first neutralizes the system by adding either Na or Cl as needed then
adds enough Na-Cl pairs
to achieve a bulk salt concentration of 150mM.

you can use it with charm (pdb/psf) or amber (parmtop/crd) formatted
files or just a pdb.
simple load up what you want before calling the script
vmd -parm7 some.parm -rst7 some.crd -e dashofsalt.vmd
vmd -pdb some.pdb -psf some.psf -e dashofsalt.vmd

NOTE: it randomly places the waters but guarantees they are separated by
5A (IONSEP)

As to the problem w/ resnames etc... I believe it handles this correctly..

see
http://dna.engr.latech.edu/~bishop/VMD/

Tom

On 06/26/2012 04:42 PM, Evgeny Bulat wrote:
> #calc_charge.py: Correctly calculates system charge based on charges
> listed directly in the PSF 

-- 
*******************************
    Thomas C. Bishop
     Tel: 318-257-5209
     Fax: 318-257-3823
    www.latech.edu/~bishop
********************************