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

venkatesh s svenkateshbioinformatics at gmail.com
Sun Sep 30 19:06:29 CEST 2012

Respected gromacs users
                                  now iam buliding the simulation system
for protein + peptide simulation (manually insert the peptide into the
protein structure file  after the TER )
following commands i used here

1. pdb2gmx  -f 2KW8.pdb -o lpvtg.gro -water tip3p -ignh -chainsep ter

in topol.top file i manually made change as a Protein_chain_A 2 (previously
it is  1)
[ molecules ]
; Compound        #mols
Protein_chain_A     2

2. editconf -f lpvtg.gro -o lpvtg_newbox.gro -c -d 1.0 -bt dodecahedron

3. genbox -cp lpvtg_newbox.gro -cs spc216.gro -o lpvtg_solv.gro -p topol.top

4. grompp -f ions.mdp -c lpvtg_solv.gro -p topol.top -o lpvtg_ions.tpr

fatal error
number of coordinates in coordinate file (lpvtg_solv.gro, 24393)
             does not match topology (topol.top, 26811)

and i read following link

manually may want update topol.top file, if yes can you explain?

kindly provide prompt solution

Thanking You


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