[gmx-users] why .top file is not updated with added waters in "gmx solvate" if customised water.gro is provided?

[ZHANG Cheng]

In the command


gmx solvate -cp 128_minimized.gro -cs water.gro -o waterbox.gro -maxsol 768 -radius 0.21 -p dppc.top


768 waters are added, resulting in the "waterbox.gro".


However, the "dppc.top" is not updated for its "[ molecules ]" section. I can of course manually add that. But why it is not automatically done?


The prompt also shows "0" for "Number of SOL molecules":


Generating solvent configuration
Will generate new solvent configuration of 3x3x3 boxes
Solvent box contains 4435 atoms in 4435 residues
Removed 1235 solvent atoms due to solvent-solvent overlap
Removed 1286 solvent atoms due to solute-solvent overlap
Sorting configuration
Found 1 molecule type:
      W (   1 atoms):   768 residues
Generated solvent containing 768 atoms in 768 residues
Writing generated configuration to waterbox.gro


Output configuration contains 2304 atoms in 896 residues
Volume                 :     421.875 (nm^3)
Density                :     639.416 (g/l)
Number of SOL molecules:      0   


Processing topology


Back Off! I just backed up dppc.top to ./#dppc.top.1#