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

[Florian Haberl]

hi,

On Wednesday 12 April 2006 09:41, santosh naik wrote:
> 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

Perhaps wrong path to your .top file or this top file is empty, check it if 
its in this directory and contains valid information.

>
> Thanking you
> Santosh Naik
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-- 
Florian
-------------------------------------------------------------------------------
 Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Mailto: florian.haberl AT chemie.uni-erlangen.de
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