[gmx-users] protein in popc

[mahbubeh zarrabi]

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



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