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

[Bratin Kumar Das]

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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