[gmx-users] Hi

[Tsjerk Wassenaar]

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 <adriana at ms.fci.unibo.it> 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
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