On 9/28/12 4:25 AM, Shine A wrote:
Sir,
I am studying the dynamics of membrane proteins using KALP-15 in DPPC.
Now I am confusing with the following ( shown at botom) part of the
tutorial.Here minimization means to minimize system_inflated.gro, is it
right? Then without .epr and .top files of system_inflated.gro how can I do
this?
You should have a topology of the system, and .mdp files are provided so you can
assemble a .tpr file and run minimization. Individual commands are not provided
at this point in the tutorial, because (as stated at the beginning of the
tutorial) it is expected that the user is familiar with a basic Gromacs
workflow, how to execute grompp and mdrun, etc.
Subsequent minimization steps are performed on system_shrink*.gro files in the
same manner.
-Justin
perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat
Note how many lipids were deleted and update the [ molecules ] directive of
your topology accordingly. Run energy minimization. Then, scale down the
lipids by a factor of 0.95 (assuming you have used default names, the
result of the minimization is called "confout.gro"):
perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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