Hi, I am doing the simulation of kalp15 in DPPC following the Justin's tutorial. In the " 2. Pack the lipids around the protein "step, to get the correct area per lipid, I enter these commands:
#perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat Updating the .top file and adding DPPC 126 to it. First minimization: Energy minimization with restrained protein #grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr #mdrun -deffnm em scale down the lipids by a factor of 0.95 #perl inflategro.pl em.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat Second minimization: #grompp -f minim.mdp -c system_shrink1.gro -p topol.top -o em_shrink1.tpr Then, I get this error: Fatal error: number of coordinates in coordinate file (system_shrink1.gro, 6400) does not match topology (topol.top, 6438) Is this not the correct command to start the second minimization? Please help me. Your suggestions are welcomed. Sincerely, Shima -- 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
