hi justin, the problem is actually InflateGro is not deleting any lipids. I had inserted the protein in lipid using VMD and saved the coordinate file and using that directly to this step
cat pro_in_pope.gro pope_whole.gro > system.gro after running perl inflategro.pl system.gro 4 POPE 14 system_inflated.gro 5 area.dat. Argument "P8" isn't numeric in printf at inflategro.pl line 708. Argument "O9" isn't numeric in printf at inflategro.pl line 708. Calculating Area per lipid... Protein X-min/max: -4 103 Protein Y-min/max: -14 100 X-range: 107 A Y-range: 114 A Building 107 X 114 2D grid on protein coordinates... Calculating area occupied by protein.. full TMD.. upper TMD.... lower TMD.... Area per protein: 107.75 nm^2 Area per lipid: 8.02906194817911 nm^2 Area per protein, upper half: 101.25 nm^2 Area per lipid, upper leaflet : 8.09202321149701 nm^2 Area per protein, lower half: 102.25 nm^2 Area per lipid, lower leaflet : 8.03790402571429 nm^2 Writing Area per lipid... Done! So please suggest me what is going wrong Regards bhavani -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
