[gmx-users] Fatal Error: number of coordinates in coordinate file does not match topology

[Tsjerk Wassenaar]

Hi Chitrita,

Please copy-paste the exact error and the command line in both cases
(working and not working). Also, what platform are you working on? Did
you by chance edit the .mdp file under windows?

Cheers,

Tsjerk

On Sat, Oct 11, 2008 at 6:46 PM, Chitrita Dutta Roy
<chitrita.md at gmail.com> wrote:
> I want to perform MD Equilibration run under position restrained for 200ps.
> Bond distances were constrained using the LINCS (Linear Constraints)
> algorithm, the water molecules were restrained using the SETTLE algorithm.
> In order to do this I have modified nsteps in original pr.mdp file.
> Following is the modified file contents:
>
>
>
> ;
>
> ; User spoel (236)
>
> ; Wed Nov 3 17:12:44 1993
>
> ; Input file
>
> ;
>
> title = Yo
>
> cpp = /usr/bin/cpp
>
> define = -DPOSRES
>
> constraints = all-bonds
>
> integrator = md
>
> dt = 0.002 ; ps !
>
> nsteps = 100000 ; total 200 ps.
>
> nstcomm = 1
>
> nstxout = 50
>
> nstvout = 1000
>
> nstfout = 0
>
> nstlog = 10
>
> nstenergy = 10
>
> nstlist = 10
>
> ns_type = grid
>
> rlist = 1.0
>
> rcoulomb = 1.0
>
> rvdw = 1.0
>
> ; Berendsen temperature coupling is on in two groups
>
> Tcoupl = berendsen
>
> tc-grps = Protein SOL
>
> tau_t = 0.1 0.1
>
> ref_t = 300 300
>
> ; Energy monitoring
>
> energygrps = Protein SOL
>
> ; Pressure coupling is not on
>
> Pcoupl = no
>
> 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
>
>
>
> Then I wanted to do grompp with this modified pr.mdp file. But it is showing
> a Fatal error like,
>
> Fatal Error:
>
> number of coordinates in coordinate file does not match topology.
>
> But if I use the original pr.mdp (without modifying it for 200ps) the grompp
> runs properly. I am not understanding what to do now. Please help me out.
>
> Thanking you,
>
> Chitrita.
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623