[gmx-users] Hi

[TJ Piggot]

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 
<tsjerkw at gmail.com> 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 <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



----------------------
TJ Piggot
t.piggot at bristol.ac.uk