[gmx-users] why no. of atoms doesn't match?

Albert mailmd2011 at gmail.com
Mon Apr 15 19:30:19 CEST 2013


  I've build a protein/membrane system with CHARMM-GUI, and I am going 
to use it for Gromacs MD simulation with Slipids FF.

First I extract the protein and generate toplogy file by command:

pdb2gmx -f protein.pdb -o gmx.pdb -ignh -ter

The protein was assigned with Amber FF including TIP3P for solvent

after that, I add the following at the top of topol.top file:

; Include forcefield parameters
#include "slipids.ff/forcefield.itp"
#include "ligand.itp"
#include "popc.itp"
#include "chol.itp"

and the following at the bottom of topol.top file:

[ molecules ]
; Compound        #mols
Protein_chain_A     1
CHL1 42
SOL 10079

A the new protein coordinate gmx.pdb was replaced CHEARMM-GUI protein 
coordinate, all cheloest are put together, all popc were also put 
together. The order in the complex.pdb are: protein, ligand, cholestrol, 
popc and water. The system contains 1 protein, 1 ligand, 42 chelostrol, 
98 POPC and 10079 water molecules. Then I am trying to minimize the 
system with command:

grompp_mpi -f em.mdp -c complex.pdb -o em.tpr

However, it always failed with messages:

Program grompp_mpi, VERSION 4.6.1
Source code file: 
/home/albert/Desktop/gromacs-4.6.1/src/kernel/grompp.c, line: 563
Fatal error:
number of coordinates in coordinate file (complex.pdb, 49531)
              does not match topology (topol.top, 51295)

I don't understand why Gromacs claim such kind of errors, since to me, 
everything is all right for my pdb file and toplogy...

thank you very much

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