On 4/2/13 5:56 AM, sdshine wrote:
Dear Users,
I have inserted protein and carbohydrate in DPPC membrane according to the
KALP
tutorials. After inserting both molecules, I checked by using VMD, the atoms
around my protein and ligand were overlapped. But I applied position
restraints to protein and ligand and run
Inflategro scripts for shrinking and packing.
Perl inflategro result
____________________
There are 3 lipids within cut-off range...
1 will be removed from the upper leaflet...
2 will be removed from the lower leaflet...
Writing scaled bilayer & centered protein...
Calculating Area per lipid...
Protein X-min/max: 11 47
Protein Y-min/max: 19 45
X-range: 36 A Y-range: 26 A
Building 36 X 26 2D grid on protein coordinates...
Calculating area occupied by protein..
full TMD..
upper TMD....
lower TMD....
Area per protein: 7.5 nm^2
Area per lipid: 10.4673818624 nm^2
Area per protein, upper half: 5.5 nm^2
Area per lipid, upper leaflet : 10.4160534349206 nm^2
Area per protein, lower half: 4.25 nm^2
Area per lipid, lower leaflet : 10.6042155870968 nm^2
Writing Area per lipid...
Done!
___________________
1st EM result
_________
---
-------
Step= 576, Dmax= 8.0e-03 nm, Epot= -9.29249e+04 Fmax= 5.95606e+03, atom=
504
Step= 578, Dmax= 4.8e-03 nm, Epot= -9.29638e+04 Fmax= 8.42117e+02, atom=
504
writing lowest energy coordinates.
Steepest Descents converged to Fmax < 1000 in 579 steps
Potential Energy = -9.2963797e+04
Maximum force = 8.4211664e+02 on atom 504
Norm of force = 4.9797871e+01
Then in EM step, showing Maximum force on certain atom.
I performed shrinking step until it converged. But every EM I have Max Force
on selected atom.
There will always be some atom with a maximum force; that's how EM works. As
long as that maximum force is below an acceptable tolerance, there is no problem.
The final complex still have unpacked lipids.
This statement doesn't make much sense to me. Either InflateGRO worked, or it
didn't. There shouldn't be any halfway.
How to correct this or whether will be corrected during Equilibration steps.
I think the problem lies in the Ist EM step itself.
Kindly give some suggestions
I don't see evidence of a problem, and certainly not within the first EM step.
-Justin
--
========================================
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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