On 1/20/19 3:04 PM, ZHANG Cheng wrote:
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
solvate is hard-coded to only recognize "SOL" explicitly. You added
something called "W," so solvate doesn't know what that is. Update your
topology manually if you're doing something non-standard (coarse-grain
systems qualify as such).
-Justin
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Justin A. Lemkul, Ph.D.
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