Your topology file does not correspond to the coordinate
file. You got to check both of them but the error is
certainly coming from the topology file. Not that you need
to include the ions.itp file after incerting the ions.
It is better to insert the ions in the solvent Temp bath
and not in a separate bath.
Your vdW cutoff is 1.0 nm. This is short if you do not do
it for a particular reason.
You do not use indexes !! grompp does not complain about
non-defined groups ??
For the last grompp you run you give the 7/out7.gro as
starting configuration (-c option) which does not seem
to be the output of your em !!
Solvating with genion is a new feature of GROMCAS ??? You
meant genbox probably.
XAvier
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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