VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jan 16 2003 - 15:11:53 CST

Hi Ioana,
  I've forwarded you question to Jim Phillips our NAMD project leader,
who is the one that developed and currently maintains the tutorial.
I think we should be able to provide a downloadable tar archive of
the tutorial that would help you get around your firewall difficulty,
Jim will get back to you on this as soon as he has a chance.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jan 15, 2003 at 07:52:27PM -0800, Ioana Cozmuta wrote:
> Hi vmd-ers,
>
> I am trying again to run the tutorial on gramicidinA step by step ( I
> remember I've tried this before and I got into troubles so I've only tried
> to learn parts that could be useful for my case).
>
> First thing first I can not run the
> eval [::http::data [::http::geturl
> http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on/control.vmd]]
>
> (security reasons). SO I have to get the "test" files myself. I've
> downloaded 1JNO.pdb from the rcsb site, I've passed the first step however
> for the structure to work I had to do an extra alias of the residue ETA in
> the pdb structure to the EDAM in the topology file. Also the FOR residue
> in the gramicidine is not present in the topology file so just to run the
> tutorial I've removed it. Then I get into the lipid section and I realize
> that I can not download the pdb file with the POPE from the site and that
> I would have to build it myself. So I was thinking to ask if it would not
> be possible to link the pdb files required to run the tutorial to the
> tutorial site so that everyone could download them? I am only interested
> from this tutorial to learn how to make use of VMD/NAMD and the TCL
> scripts so I do not want to invest too much time in fixing the structure
> or generating the pdb files required to run the tutorial.
>
> I hope you will not mind my suggestion.
> Thank you,
> Ioana
>
>
> ****************************************************************************
> * Ioana Cozmuta, PhD * *
> * NASA-AMES Research Center * "Gravitation can not be held responsible*
> * Mail Stop 230-3 * for people falling in love" *
> * Moffet Field,CA 94035 * *
> * phone: (650) 604-0993 * Albert Einstein*
> * fax: (650) 604-0350 * (1879-1955) *
> **************************************************************************** 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
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