Hello:
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
LIG 1
CHL1 42
POPC 98
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
Albert
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