[gmx-users] problem while running grompp Pocition restrined dynamics

[santosh naik]

hi
i am working with the spider toxin protein and  as mentioned early i
was unable 2 over come this process
below i have mentioning my problem in detail
first i take the protein and run the pdb2 gmx command under the
gromacs force field
pdb2gmx -f spider.pdb -o 1/out1.gro -p 1/out1.top
editconf -bt octahedron -f 1/out1.gro -o 2/out2.gro -c -d 0.7
then i solvates the box using genion
genion -cp 2/out2.gro -cs spc216.gro  -o  3/out3.gro -p 1/out1.top
then i run the grompp for energy minimisation using the em.mdp file given below
title               =  drg_trp
cpp                 =  /usr/bin/cpp
define              =  -DFLEX_SPC
constraints         =  none
integrator          =  steep
dt                  =  0.002    ;  ps !
nsteps              =  500
nstlist             =  10
ns_type             =  grid
rlist               =  0.9
coulombtype         =  PME ; Use particle-mesh ewald
rcoulomb            =  0.9
rvdw                =  1.0
fourierspacing      =  0.12
fourier_nx          =  0
fourier_ny          =  0
fourier_nz          =  0
pme_order           =  4
ewald_rtol          =  le-5
optimize_fft        =  yes
;
;      Energy minimizing stuff
;
emtol               = 1000.0
emstep              =  0.01
grompp -f em.mdp -c 3/out3.gro -p 1/out1.top -o 4/out4.tpr
NOTE:
  System has non-zero total charge: 2.000000e+00

hen i used the genion command
genion -s 4/out4.tpr -o 5/out5.gro  -nname Cl -nn 2 -g 5/out5.log
now again i run the grompp now here i have edited the top file i
removed 2 water molecule and added 2 cl molecules
grompp -f em.mdp -c 5/out5.gro -p 1/out1.top -o 6/out6.tpr
nohup mdrun -s 6/out6.tpr -o 7/out7.trr -c 7/out7.gro -g 7/out7.log -e
7/out7.edr &
then i tried to run the position restrained dynamic so i have tried with grompp
using mdp file given below
title               =  trp_drg
warnings            =  10
cpp                 =  /lib/cpp ; location of cpp on SGI
define              =  -DPOSRES
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002  ; ps !
nsteps              =  10000  ; total 20.0 ps.
nstcomm             =  1
nstxout             =  250 ; output coordinates every 0.5 ps
nstvout             =  1000 ; output velocities every 2.0 ps
nstfout             =  0
nstlog              =  10
nstenergy           =  10
nstlist             =  10
ns_type             =  grid
rlist               =  0.9
coulombtype         =  PME
rcoulomb            =  0.9
rvdw                =  1.0
fourierspacing     =  0.12
fourier_nx         =  0
fourier_ny         =  0
fourier_nz         =  0
pme_order          =  6
ewald_rtol         =  1e-5
optimize_fft       =  yes
; Berendsen temperature coupling is on in four groups
Tcoupl              =  berendsen
tau_t               =  0.1       0.1   0.1   0.1
tc_grps             =  protein   IN4   sol   Cl-
ref_t               =  300       300   300   300
; Pressure coupling is on
Pcoupl              =  berendsen
pcoupltype          =  isotropic
tau_p               =  0.5
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
grompp -f pr.mdp -c 7/out7.gro -p 1/out1.top -o 8/out8.tpr
here i got he error
Fatal error:
number of coordinates in coordinate file (7/out7.gro, 7485)
does not match topology (1/out1.top, 0)
can any one help me over this issue

Thanking you
Santosh Naik