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

[Justin Lemkul]

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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