[gmx-users] Membrane protein tutorial

[Pawan Kumar]

Hello sir,

Thanks for such a explanatory tutorial.
I am stuck with one error now.
I have protein, popc, sol and cl- in my system.
I have merged the sol and cl- using make_ndx.
But when I run grompp I get the error like this "popc not defined in the
index file".
The grompp command : grompp -f pr.mdp -c box_em.pdb -p topol.top -o
box_pr.tpr
Any suggestions please.
*
pr.mdp file :*
title               =  protein in popc bilayer
cpp                 =  /usr/bin/cpp
define              =  -DPOSRES -DPOSRES_LIPID
constraints         =  all-bonds
constraint-algorithm=  Lincs
integrator          =  md
dt                  =  0.002
nsteps              =  5000
nstcomm             =  1
nstxout             =  50
nstvout             =  1000
nstfout             =  0
nstlog              =  10
nstenergy           =  10
nstlist             =  10
ns_type             =  grid
rlist               =  1
coulombtype         =  PME
rcoulomb            =  1
vdw-type            =  Cut-off
rvdw                =  1
; Berendsen temperature coupling is on in two groups
tcoupl              = berendsen
tc_grps             = Protein POPC SOL_CL-
tau_t               = 0.1 0.1 0.1
ref_t               = 300 300 300
; Energy monitoring
energygrps        =  Protein POPC SOL_CL-
; Pressure coupling is on
;Pcoupl              =  berendsen
tau_p               =  2.0 2.0
compressibility     =  4.5e-5 4.5e-5
ref_p               =  1.0 1.0
Pcoupl_type         =  semiisotropic
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529

Thanking you,
Pawan
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