[gmx-users] problem while running grompp Pocition restrined dynamics

[X.Periole]

Your topology file does not correspond to the coordinate
file. You got to check both of them but the error is 
certainly coming from the topology file. Not that you need
to include the ions.itp file after incerting the ions.

It is better to insert the ions in the solvent Temp bath
and not in a separate bath.

Your vdW cutoff is 1.0 nm. This is short if you do not do
it for a particular reason.

You do not use indexes !! grompp does not complain  about
non-defined groups ??

For the last grompp you run you give the 7/out7.gro as
starting configuration (-c option) which does not seem
to be the output of your em !!

Solvating with genion is a new feature of GROMCAS ??? You
meant genbox probably.

XAvier

> hi guys
> i am working with the spider toxin protein and  as 
>mentioned early i
> was unable 2 over come this process
> 
> below i have mentioning my problem in detail
> 
> first i take the protein and run the pdb2 gmx command 
>under the
> gromacs force field
> 
> pdb2gmx -f spider.pdb -o 1/out1.gro -p 1/out1.top
> 
> then i run the edit conf
> 
> editconf -bt octahedron -f 1/out1.gro -o 2/out2.gro -c 
>-d 0.7
> 
> then i solvates the box using genion
> genion -cp 2/out2.gro -cs spc216.gro  -o  3/out3.gro -p 
>1/out1.top
> 
> then i run the grompp for energy minimisation
> using the em.mdp file given below
> 
> title               =  drg_trp
> cpp                 =  /usr/bin/cpp
> define              =  -DFLEX_SPC
> constraints         =  none
> integrator          =  steep
> dt                  =  0.002    ;  ps !
> nsteps              =  500
> nstlist             =  10
> 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
> ;
> ;      Energy minimizing stuff
> ;
> emtol               = 1000.0
> emstep              =  0.01
> 
> 
> grompp -f em.mdp -c 3/out3.gro -p 1/out1.top -o 
>4/out4.tpr
> 
> here i got one note
> NOTE:
>  System has non-zero total charge: 2.000000e+00
> 
> then i used the genion command
> genion -s 4/out4.tpr -o 5/out5.gro  -nname Cl -nn 2 -g 
>5/out5.log
> 
> now again i run the grompp
> now here i have edited the top file
> i removed 2 water molecule and added 2 cl molecules
> grompp -f em.mdp -c 5/out5.gro -p 1/out1.top -o 
>6/out6.tpr
> 
> then i have run the mdrun
> nohup mdrun -s 6/out6.tpr -o 7/out7.trr -c 7/out7.gro -g 
>7/out7.log -e
> 7/out7.edr &
> 
> then i tried to run the position restrained dynamic so i 
>have tried with grompp
> 
> using mdp file given below
> title               =  trp_drg
> warnings            =  10
> cpp                 =  /lib/cpp ; location of cpp on SGI
> define              =  -DPOSRES
> constraints         =  all-bonds
> integrator          =  md
> dt                  =  0.002  ; ps !
> nsteps              =  10000  ; total 20.0 ps.
> nstcomm             =  1
> nstxout             =  250 ; output coordinates every 
>0.5 ps
> nstvout             =  1000 ; output velocities every 
>2.0 ps
> nstfout             =  0
> nstlog              =  10
> nstenergy           =  10
> nstlist             =  10
> ns_type             =  grid
> rlist               =  0.9
> coulombtype         =  PME
> rcoulomb            =  0.9
> rvdw                =  1.0
> fourierspacing     =  0.12
> fourier_nx         =  0
> fourier_ny         =  0
> fourier_nz         =  0
> pme_order          =  6
> ewald_rtol         =  1e-5
> optimize_fft       =  yes
> ; Berendsen temperature coupling is on in four groups
> Tcoupl              =  berendsen
> tau_t               =  0.1       0.1   0.1   0.1
> tc_grps             =  protein   IN4   sol   Cl-
> ref_t               =  300       300   300   300
> ; Pressure coupling is on
> Pcoupl              =  berendsen
> pcoupltype          =  isotropic
> tau_p               =  0.5
> compressibility     =  4.5e-5
> ref_p               =  1.0
> ; Generate velocites is on at 300 K.
> gen_vel             =  yes
> gen_temp            =  300.0
> gen_seed            =  173529
> 
> grompp -f pr.mdp -c 7/out7.gro -p 1/out1.top -o 
>8/out8.tpr
> 
> here i got he error
> 
>Fatal error:
> number of coordinates in coordinate file (7/out7.gro, 
>7485)
>             does not match topology (1/out1.top, 0)
> 
> can any one help me over this issue
> 
> Thanking you
> Santosh Naik
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