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

[Kevin Boyd]

Hi,

The hard-coded SOL reference that Justin mentioned has been fixed in Gromacs 2018.3 and 2019. If you upgrade your gromacs version, gmx solvate should work as intended.

Kevin

> On Jan 20, 2019, at 3:11 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
>> 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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