dear freinds I have made a hole in POPC128a bilayer.But I failed inputing protein into it.I run below commands but there is not protein in the hole.whould you please help me? do you have another protocol for protein insertion in popc (in detail)?
make_hole.pl -f popc.pdb -o popcout.pdb -r 1.4 -lipat P8 -lipid POP -cx 2.3 -cy 2.8 grompp -f run.mdp -o insert.tpr -c popcout.pdb -p popc.top mdrun -v -hole -holep hp.mdp -deffnm insert ----------------------------------------------------- popc.top is here: ; Topology for a pure POPC bilayer with 106 lipids and 2460 water molecules #include "ffgmx.itp" ; #include "lipid.itp" #include "popc.itp" #ifdef FLEX_SPC #include "flexspc.itp" #else #include "spc.itp" #endif [ system ] ; name Pure POPC bilayer with 106 lipids and 2460 water molecules [ molecules ] ; name number POPC 106 SOL 2460 ------------------------------------------------------ popc.mdp is here : ; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; title = POPC128a cpp = /lib/cpp define = -DPOSRES -DFLEX_SPC dt = 0.002 ; ps! nsteps = 50000 ; total 10 ns. nstcomm = 1 integrator = md ; Output control nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 5000 nstenergy = 5000 ; Neighbor searching nstlist = 10 ns_type = grid rlist = 1.0 pbc = xyz ; Bonds constraints = all-bonds constraints_algorithms = lincs unconstrained_start = no lincs_order = 4 lincs_iter = 1 lincs_warnangle = 30 ; Electrostatics and VdW coulombtype = PME rcoulomb = 1.0 rvdw = 1.0 fourierspacing = 0.12 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = POPC SOL tau_t = 0.1 0.1 ref_t = 300 300 ; Energy monitoring energygrps = POPC SOL ; Pressure coupling Pcoupl = berendsen pcoupltype = isotropic tau_p = 1 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 ------------------------------------------------------ hp.mdp is here: holetype = MSMS hfm = 10 supf = 10 molsurf_log = gsurf.log hr = 0 hx = 0 hy = 0 hz = 5.0 hp1 = 1 hp2 = 2120 s1 = 0 s2 = 0 hz1 = 3.3 hz2 = 7.3 sfm = 10.0 sofs = 0.15 molsurf_file = /home/zarrabi/msms/com18 debugsurf = no resforces = yes ------------------------------------------------------ best regards 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
