VMD-L Mailing List

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Wed Jan 15 2003 - 21:52:27 CST

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

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* Ioana Cozmuta, PhD * *
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