[gmx-users] Hi

[Adriana Pietropaolo]

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 
_____________________________________________