Hi, 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. Sincerely, Shima -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists