Sara baretller wrote:
HI
in the tutorial , it says that the script has the instructions to follow
but when i opened the script i didn't find any instructions
please what does 14 stands for and 5
perl inflategro.pl <http://inflategro.pl> system.gro 4 DPPC 14
system_inflated.gro 5 area.dat
14 is a cutoff radius for deleting lipids. 5 is the grid spacing for the area
measurement, if memory serves. Both terms are in Angstrom.
-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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