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

[paul buscemi]

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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