Dear Santosh,
check what forcefield u have used...
whatever forcefield u use, add ions as per its recommended format
specified in ions.itp. Read ions.itp carefully... if it is GROMOS96,
u have to change Na to NA+ and likewise...
all the best...
bharat
On Wed, 5 Apr 2006, santosh naik wrote:
hi
today i have tried with some other protein but the problem still persists .
today i will tell you problem in detail
today i have taken the protein pdb file which conatains only the amino
acids no hetero atoms
i have run the pdb2gmx command
pdb2gmx -f 1.pdb -o 1/out1.top -p 1/out1.top -i 1/out1.itp -n
1/out1.ndx -q 1/out1.pdb
i got all the 5 files
later i used the command edit conf
editconf -bt octahedron -f 1/out1.gro -o 2/out2.gro -c -d 0 .7
then i run the genbox
genbox -cp 2/out2.gro -cs spc216.gro -o 3/out3.gro -p 1/out 1.top
here i got the gro file and modified top file
then i have run the grompp
grompp -f em.mdp -c 3/out3.gro -p 1/out1.top -o 4/out4.tpr
my mdp file is
bellow
##########################################################
title = drg_trp
cpp = /usr/bin/cpp
define = -DFLEX_SPC
constraints = none
integrator = steep
dt = 0.002 ; ps !
nsteps = 1000
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
Tcoupl = no
Pcoupl = no
gen_vel = no
;
; Energy minimizing stuff
;
emtol = 1000.0
emstep = 0.01
###############################################################
There i got one NOTE : System has non-zero total charge: -6.999998e+00
later i tried to run the mdrun but the process fails at 24 steps
Then i used the genion
genion -s 4/out4.tpr -o 5/out5.gro -pname Na -np 7 -g 5/out 5.log
here i got the modified gro file
but tere was warning that
turning of free energy, will use lambda=0
Then i have edited the top file i got according to the gro file
since i m using the gromacs 3.3 the #include ions.itp was default
so i have removed the 7 water atoms from the top file and added 7 Na atoms
and run the grompp
grompp -f em.mdp -c 5/out5.gro -p 1/out1.top -o 6/out6.tpr
here the programme was failed showing the error
Fatal error:
No such moleculetype Na
i have checked the ions .itp
its having the information Na atom than why its showing this i could
n't understand
can any one help me over this here i have attatched my out6.gro file
and the top file
Thanking you
Santosh Naik
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