[gmx-users] grompp in KALP15-DPPC

Shima Arasteh shima_arasteh2001 at yahoo.com
Sat Aug 25 18:26:01 CEST 2012

I am doing the simulation of KALP15 in DPPC following the Justin's tutorial.

For the step of solvation I ran this command:
# genbox -cp system.gro -cs spc216.gro -o system_solv.gro -p topol.top

The output of this step is as here:
Reading solute configuration
frame t= 1.000
Containing 17503 atoms in 3800 residues
Initialising van der waals distances...

WARNING: masses and atomic (Van der Waals) radii will be determined
         based on residue and atom names. These numbers can deviate
         from the correct mass and radius of the atom type.

Reading solvent configuration
"216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984"
solvent configuration contains 648 atoms in 216 residues

Initialising van der waals distances...
Will generate new solvent configuration of 4x4x4 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
    SOL (   3 atoms): 13824 residues
Calculating Overlap...
box_margin = 0.315
Removed 10608 atoms that were outside the box
Neighborsearching with a cut-off of 1.125
Table routines are used for coulomb: FALSE
Table routines are used for vdw:     FALSE
Cut-off's:   NS: 1.125   Coulomb: 1.125   LJ: 1.125
System total charge: 0.000
Grid: 18 x 18 x 18 cells
Successfully made neighbourlist
nri = 152829, nrj = 41861902
Checking Protein-Solvent overlap: tested 3204927 pairs, removed 30048 atoms.
Checking Solvent-Solvent overlap: tested 17610 pairs, removed 60 atoms.
Added 252 molecules
Generated solvent containing 756 atoms in 252 residues
Writing generated configuration to system_solv.gro

Back Off! I just backed up system_solv.gro to ./#system_solv.gro.3#
frame t= 1.000

Output configuration contains 18259 atoms in 4052 residues
Volume                 :     272.811 (nm^3)
Density                :      947.87 (g/l)
Number of SOL molecules:   3907   

Processing topology
Removing line #929 'SOL               533' from topology file (topol.top)

Then running grompp for the next step ( neutralization )

grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr

But the error is:

Fatal error:
number of coordinates in coordinate file (system_solv.gro, 18259)
             does not match topology (topol.top, 18159)
For more information and tips for troubleshooting, please check the GROMACS

Would you pleas help me? Do I need to modify the .top file before running grompp?

Thanks for your suggestions in advance.


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