Dear freinds There are some errors when I run grompp. I try to use make_hole program to make a hole in POPC. ./make_hole.pl -f popc128a.pdb -o popc.pdb -r 1.4 -lipat P8 -lipid POPC -cx 2.3 -cy 2.8 editconf -f popc.pdb -o popc.gro editconf -bt cubic -f popc.gro -o popc.gro -c -d 0.5 genbox -cp popc.gro -cs spc216.gro -o popc_b4em.gro -p popc.top This is my popc.top after genbox. #include "ffgmx_lipid.itp" #include "popc.itp" ;#include "ions.itp"
#ifdef POSRES #include "lipid_posre.itp" #endif #ifdef FLEX_SPC #include "flexspc.itp" #else #include "spc.itp" #endif [ system ] ; name popc + h2o [ molecules ] ; name number POPC 106 There is my em.mdp file. cpp = /lib/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 100 ; ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb = 1.0 rvdw = 1.0 Tcoupl = no Pcoupl = no gen_vel = no grompp -f em.mdp -c popc_b4em.gro -p popc.top -o popc.tpr After doing these, error message is appeare: popc.top:1:27: error: ffgmx_lipid.itp: No such file or directory popc.top:2:20: error: popc.itp: No such file or directory cpp exit code: 256 Tried to execute: '/lib/cpp -I/usr/local/gromacs/share/top -DFLEX_SPC popc.top > gromppzaUDO1' The '/lib/cpp' command is defined in the .mdp file processing topology... Cleaning up temporary file gromppzaUDO1 ------------------------------------------------------- Program grompp, VERSION 3.3.1 Source code file: topio.c, line: 388 Fatal error: Invalid order for directive moleculetype, file ""/usr/local/gromacs/share/top/flexspc.itp"", line 1 best regard zarrabi __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php