I believe you want to make a NAMD compatible version.
You can easily do it using VMD Automated PSF generation plugin more details
here
http://www.ks.uiuc.edu/Research/vmd/plugins/autopsf/
More details on how to do it here
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-html/node6.html
Video here
http://www.youtube.com/watch?v=BKy2l_HpgEU
If you know the dimension and type of waterbox then why you are trying to
generate one separately for water box as you can do it platform
independently.
On Mon, May 5, 2014 at 10:44 AM, sammia khatak <saammia_kt.hotmail.com>wrote:
> Hello
> I am running energy minimization of protein ligand complex. Is there a way
> to generate psf file from pdb file which is actually a protein ligand
> complex in water box and if it is so then how? secondly either way if i
> just generate psf file of protein ligand complex separately and waterbox
> separately. will it work?
> suggest eitherway.
>
> Thanks
> samia
>
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Thanks & Regards;
Soumendranath Bhakat
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Received on Mon May 05 2014 - 02:30:02 PDT
