VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Feb 12 2010 - 00:00:21 CST

Hi,
  You can start out by using the AutoPSF plugin in VMD to try
and build your structure, optionally adding ions etc. It's not
clear from your email precisely what you are looking for, but
generally speaking you need to go through multiple steps to
build a complete structure, generating the PSF is really just
the last step, and perhaps the most mechanical. I would suggest
that you read through the NAMD/VMD tutorials, in particular
the ones related to structure building:
  http://www.ks.uiuc.edu/Training/Tutorials/
 
Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Feb 10, 2010 at 05:28:45PM +0530, zubin mehta wrote:
> How can I create a psf file along with some other atoms like Ca which need
> to be incorporated?
> Generally, I get only the protein part on generating the psf. Is there any
> way out?
>
> --
> Zubin Mehta
> 5th year UG
> IIT Bombay
> zubinmehta.wordpress.com
>
> --
> "For millions of years
> mankind lived just like the animals.
> Then something happenend
> which unleashed the power of our imagination.
> We learned to talk." 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078