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. The final complex still have unpacked lipids. 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 Thanks in advance -- View this message in context: http://gromacs.5086.n6.nabble.com/Maximum-force-on-atom-and-unpacked-lipids-tp5006817.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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
