[gmx-users] Hi

[santosh naik]

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