Sara baretller wrote:
Hi so i did
Remove unnecessary lines (the box vectors from the KALP structure, the
header information from the DPPC structure) and update the second line
of the coordinate file (total number of atoms) accordingly. After i use
the
cat KALP_newbox.gro dppc128_whole.gro > system.gro
when i check the file system.gro it has the protein and the lipid coordinates, however when i load to vmd to veiw , the VMD does not show anything , does any body have an idea what s wrong
Then the file format is still broken in some way.
-Justin
Thank you
On Wed, Aug 17, 2011 at 4:19 PM, Sara baretller
<sarabiocomputat...@gmail.com <mailto:sarabiocomputat...@gmail.com>>
wrote:
ok i did find the script
thank you
On Wed, Aug 17, 2011 at 4:03 PM, Sara baretller
<sarabiocomputat...@gmail.com
<mailto:sarabiocomputat...@gmail.com>> wrote:
Thank you
yes i removed the Remove unnecessary lines ... i found the
inflategro.pl <http://inflategro.pl/>
when i click on the rl inflategro.pl
<http://inflategro.pl/> it gives me Firefox can't find the
server at inflategro.pl <http://inflategro.pl>.
<http://inflategro.pl/>
On Wed, Aug 17, 2011 at 3:17 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>> wrote:
Sara baretller wrote:
I am doing the protein in lipid tutorial .
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin/__gmx-tutorials/membrane___protein/02_topology.html
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html>
Pack the lipids around the protein, i dont see where
is the script perl inflategro.pl
<http://inflategro.pl> <http://inflategro.pl>
I googled It and did not find it. Can you please
send me the script or tell me where I can find it
Then Google again :) If you search "Inflategro" it is
the first result that comes up.
Also I used the cat KALP_newbox.gro
dppc128_whole.gro > system.gro
so I checked the system.gro in vmd and did not load
anything. I was able to vew the KALP_newbox.gro and
the dppc128_whole.gro but not the system.gro
do I have to organize the system.gro because I can
see that the protein in numbered from 1 to … then
the lipids start from 1 ….end .. will that cause a
problem
Numbering is irrelevant. You probably didn't clean up
the file as instructed in the tutorial:
"Remove unnecessary lines (the box vectors from the KALP
structure, the header information from the DPPC
structure) and update the second line of the coordinate
file (total number of atoms) accordingly."
-Justin
--
==============================__==========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
==============================__==========
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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