Hi All,<br><br>I am having a trouble during EM step after I inflategro my lipid.gro (protein is already centered). <br><br>After doing this : <br><br>Reading..... <br>
Scaling lipids.... <br>There are 512 lipids... <br>
with 14 atoms per lipid.. <br><br>Determining upper and lower leaflet...<br>240 lipids in the upper... <br>
272 lipids in the lower leaflet <br><br>Centering protein....<br>Checking for overlap....<br>...this might actually take a while....<br>100 % done... <br>There are 0 lipids within cut-off range...<br>
0 will be removed from the upper leaflet...<br>0 will be removed from the lower leaflet...<br><br>Writing scaled bilayer & centered protein...<br><br><br>Calculating Area per lipid...<br>Protein X-min/max: 0 133<br>
Protein Y-min/max: 0 133<br>X-range: 133 A Y-range: 133 A<br>Building 133 X 133 2D grid on protein coordinates...<br>Calculating area occupied by protein..<br>full TMD..<br>upper TMD....<br>lower TMD....<br>Area per protein: 115 nm^2<br>
Area per lipid: 10.6034139525 nm^2<br><br>Area per protein, upper half: 82 nm^2<br>Area per lipid, upper leaflet : 11.447808216 nm^2<br><br>Area per protein, lower half: 69.25 nm^2<br>Area per lipid, lower leaflet : 10.1478822494118 nm^2<br>
<br>Writing Area per lipid...<br>Done!<br><br>This shows that there are no clashes between lipid and protein but when I run EM after this step it gives me lots of lincs warning and errors. I don't know why is that happening and I am using em.mdp file provided by MARTINI because I am working on Coarse Grained. Please help me out if what changes do I need to make to get rid off LINCS.<br>
<br>Thanks,<br><br>Sunny<br>