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

[mary ko]

Hello paulI think you didnt read my question precisely. I omitted one chain and saved the .pdb. in the new pdb file residue numbers start from 13 while atom numbers are correct starting from 1. I have 2 ligands in the file and created the topology without them and then added 'lig1-lig2.itp' in the topology file and also lig1   1 lig2    1 at the end in [molecules]. In other files i have starting from residue number 1 i dont face that error but in the present one i get this error. I wanted to be sure if residue number is the source of problem since sorting the numbers is a hard task.

    On Thursday, May 16, 2019, 3:29:53 PM PDT, 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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