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

Bratin Kumar Das 177cy500.bratin at nitk.edu.in
Fri May 17 03:54:07 CEST 2019


Hi
   This error is coming due to mismatch in coordinates..I think you didn't
delete chain In the gro file. First make the starting structure properly

On Fri 17 May, 2019, 4:00 AM paul buscemi, <pbuscemi at q.com> wrote:

> Gromacs is telling you what to do.Make a new top file
>
> I do not think you can start a pdb from other than position 1 and the top
> must match exactly. it is probably more straightforward to  delete the
> chain and save the pdb. Use pdb2gmx to recreate the top.
>
>
> good luck
>
> > On 16,May 2019, at 1:13 PM, mary ko <maryko2019 at yahoo.com> wrote:
> >
> > Hello all
> > I want to run a simulation of a protein from PDB data bank with a
> ligand. It has two chains and I need only chain A. when I delete chain B in
> CHIMERA and try to run the simulation, it stops at the gmx_mpi grompp -f
> ions.mdp -c solve.pdb -p topol.top -o ions.tpr step with the error of
> number of coordinates in the solve.pdb (143982) does not match the
> topol.top (143983). I checked the .pdb file and it starts from residue 13.
> Do I get the error because of that residues not being sorted from 1, since
> I use the same method for the sorted files and they run without
> errors.Thank you
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