Hi
I had the same problem i needed NA in the .gro (get this by in genion
having -pname NA)
hope this help
Tom
--On Wednesday, April 05, 2006 15:38:22 +0200 Tsjerk Wassenaar
<[EMAIL PROTECTED]> wrote:
Hi :)
Not the box, you probably need NA or NA+. It's case sensitive and depends
on the force field definition you use.
Cheers,
Tsjerk
On 4/5/06, Adriana Pietropaolo <[EMAIL PROTECTED]> wrote:
Probably you generated a bad box.
Check the box with i.e. rasmol and try to use -princ option in editconf
(to put the protein in its inertial axes) and genion to make the ions to
ensure charge neutrality.
good luck,
Adriana
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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--
_____________________________________________
Adriana Pietropaolo,
PhD student,
dipartimento di Chimica Fisica ed Inorganica,
Facolta' di Chimica Industriale
Universita' di Bologna
WEB:www2.fci.unibo.it/~adriana
Tel 051/6446992
FAX 051/2093690
_____________________________________________
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--
Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
----------------------
TJ Piggot
[EMAIL PROTECTED]
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