From: Axel Kohlmeyer (
Date: Mon Sep 19 2011 - 07:01:15 CDT

On Mon, 2011-09-19 at 16:31 +0530, madhumita das wrote:
> Dear VMD Users,
> I have generated water molecules to add in the
> protein cavities using DOWSER , after that I added dowserwater pdb
> file to the protein file but when I go to generate psf file for the
> whole complex it fails to generate coordinates,I tried so many times

this is not how you do it. check out the NAMD/psfgen documentation
and tutorials. they deal with multi-component systems, e.g. water

> but unable to genarate psf file,Is it possible to run simulation
> without genarating psf files? Please help me.

you obviously don't understand what information is provided or
missing in the psf and pdb file. this, however, is important to
understand what happens in MD simulations. again, the solution
to this problem is to first teach yourself more about what NAMD
and psfgen do and need to work properly and the user's guides
and tutorials are the best place to start.


> Yours faithfully,
> Madhumita Das