[gmx-users] Hi

[bharat v. adkar]

Dear Santosh,
check what forcefield u have used...
whatever forcefield u use, add ions as per its recommended format 
specified in ions.itp. Read ions.itp carefully... if it is GROMOS96, 
u have to change Na to NA+ and likewise...

all the best...

bharat


On Wed, 5 Apr 2006, santosh naik wrote:

> 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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