On 11/1/12 11:20 PM, vidhya sankar wrote:
As uou Told me in the Previous Mail I have Given My sereis of Commands With
Real file Names
./pdb2gmx_d -f 2KDQ.pdb -o 2KDQ.gro -ignh -ter -water spc
./editconf_d -f 2KDQ.gro -o 2KDQ_newbox.gro -box 6 6 6 -c
./editconf_d -f dppc128.pdb -o dppc128n.gro -center 3 3 3 -box 6 6 6
./grompp_d -f emdppc.mdp -c dppc128n.gro -p topol_dppc.top -o emdppc.tpr
-maxwarn 1
./trjconv_d -s emdppc.tpr -f dppc128n.gro -o dppc128_whole.gro -pbc mol
-ur compact
./editconf_d -f 2KDQ.gro -o 2KDQ_newbox.gro -box 6 6 6 -c
cat 2KDQ_newbox.gro dppc128_whole.gro > system.gro
./genrestr_d -f 2KDQ_newbox.gro -o strong_posre.itp -fc 100000 100000 100000
perl inflategro.pl system.gro 4 DPPC 18 system_inflated.gro 5 area.dat
./grompp_d -f emdppc.mdp -c system_inflated.gro -p 2KDQ.top -o 2KDQDPPCem.tpr
./mdrun_d -v -deffnm 2KDQDPPCem
perl inflategro.pl 2KDQDPPCem.gro 0.95 DPPC 0 system_inflated1.gro 5
area1.dat
./grompp_d -f emdppc.mdp -c system_inflated1.gro -p 2KDQ.top -o
2KDQDPPCem1.tpr
./mdrun_d -v -deffnm 2KDQDPPCem1
perl inflategro.pl 2KDQDPPCem1.gro 0.95 DPPC 0 system_inflated2.gro 5 area2.dat
./grompp_d -f emdppc.mdp -c system_inflated2.gro -p 2KDQ.top -o
2KDQDPPCem2.tpr
./mdrun_d -v -deffnm 2KDQDPPCem2
perl inflategro.pl 2KDQDPPCem2.gro 0.95 DPPC 0 system_inflated3.gro 5 area3.dat
output for My satisfactorily shrunken system as follows
Reading.....
Scaling lipids....
There are 127 lipids...
with 50 atoms per lipid..
Determining upper and lower leaflet...
64 lipids in the upper...
63 lipids in the lower leaflet
Centering protein....
Writing scaled bilayer & centered protein...
Calculating Area per lipid...
Protein X-min/max: 98 119
Protein Y-min/max: 99 117
X-range: 21 A Y-range: 18 A
Building 21 X 18 2D grid on protein coordinates...
Calculating area occupied by protein..
full TMD..
upper TMD....
lower TMD....
Area per protein: 3.75 nm^2
Area per lipid: 6.60886502362205 nm^2
Area per protein, upper half: 2.75 nm^2
Area per lipid, upper leaflet : 6.572858265625 nm^2
Area per protein, lower half: 3 nm^2
Area per lipid, lower leaflet : 6.67322109523809 nm^2
Writing Area per lipid.
./grompp_d -f emdppc.mdp -c system_inflated3.gro -p 2KDQ.top -o
2KDQDPPCem3.tpr
./mdrun_d -v -deffnm 2KDQDPPCem3
In the final Energy minimization (2KDQDPPCem3.gro file) of the satisfactorily
shrunken
system The Box vectors Has been Increased form 6 6 6 6 to
20.57700 20.57700 6.00000
As you're suspecting I may be confusing your files. In the beginning I am
giving Series of Commands with Real files Name
Could you Please Suggests Where i Have Confused in File Names ? Kindly Give
me your Valuable Suggestion
Now it is clear to me that you're simply not done. Three iterations of
shrinking is not satisfactory. 6.57 nm^2 = 657 A^2. Mind the square term in
the conversion factor. You have a long way to go yet. Simple visualization of
the system should have made this obvious.
-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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