[gmx-users] problem while running grompp Pocition restrined dynamics
santosh naik
btsanty at gmail.com
Wed Apr 12 09:41:28 CEST 2006
hi guys
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
then i run the edit conf
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
here i got one note
NOTE:
System has non-zero total charge: 2.000000e+00
then 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
then i have run the mdrun
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
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