[gmx-users] About Lipid Protein simualtion

[vidhya sankar]

Dear Justin ,
                     Thank you for you Previous reply.  


I am doing  Simulation of Cyclic Peptide in Lipids  I am following your tutorial  When I use inflategro script For my System I have got Output System_inflated.gro file with certain message in Command prompt as follows  . The Below Message Shows That There is No Lipid Molecules Are Deleted  Should I Change the Cut-off or scaling Factor  to Delete the Lipid Molecules or is it enough ,  I Mean  Must Some Lipid Molecules Need to be Deleted ?


There are 128 lipids...
with 50 atoms per lipid..
Determining upper and lower leaflet...
64 lipids in the upper...
64 lipids in the lower leaflet 
Centering protein....
Checking for overlap....
...this might actually take a while....
100 % done...
There are 0 lipids within cut-off range...
0 will be removed from the upper leaflet...
0 will be removed from the lower leaflet...
Writing scaled bilayer & centered protein...
Calculating Area per lipid...
Protein X-min/max: 19    40
Protein Y-min/max: 21    39
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: 4 nm^2
Area per lipid: 8.9375 nm^2
Area per protein, upper half: 3.5 nm^2
Area per lipid, upper leaflet : 8.9453125 nm^2
Area per protein, lower half: 3.5 nm^2
Area per lipid, lower leaflet : 8.9453125 nm^2
Writing Area per lipid...
Done!

2) Also When I Run Grompp for EM Which Topology Should  I use ?  I have  used my Multi chain     protein.top When I Have used that I got Error AS follows
Fatal error:

[ file strong_porse.itp, line 8 ]:
Atom index (4) in position_restraints out of bounds (1-3).
This probably means that you have inserted topology section "position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.
For more information and tips for troubleshooting, please check the GROMACS

How to Rectify the Problem?


Thanks In Advance 

With High Regards 

S.Vidhyasankar