[gmx-users] desired no of water molecules

[tarak karmakar]

Thanks for the quick reply, I have given this command to add 612 water
molecules.
genbox -cs spc216 -nmol 612 -cp ala_box.gro -o ala_solv.gro -p ala.top

But in the solvated file, I see there are 668 water molecules.
A part of the output while adding water molecules is as follows

 Using plugin gro for structure file ala_solv.gro
Info) Using plugin gro for coordinates from file ala_solv.gro
Info) Determining bond structure from distance search ...
Info) Finished with coordinate file ala_solv.gro.
Info) Analyzing structure ...
Info)    Atoms: 2026
Info)    Bonds: 1357
Info)    Angles: 0  Dihedrals: 0  Impropers: 0  Cross-terms: 0
Info)    Bondtypes: 0  Angletypes: 0  Dihedraltypes: 0  Impropertypes: 0
Info)    Residues: 671
Info)    Waters: 668
Warning) Unusual bond between residues:  1 (none) and 2 (protein)
Warning) Unusual bond between residues:  2 (protein) and 3 (none)
Info)    Segments: 1
Info)    Fragments: 669   Protein: 1   Nucleic: 0


On Tue, Aug 14, 2012 at 9:46 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> On 14/08/2012 2:02 PM, tarak karmakar wrote:
>>
>> Dear All,
>>
>> Is there any way to add a specific number of water ( let say 650
>> water) molecules while dissolving the solute in a given box ?
>
>
> Check out genbox -h
>
> Mark
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Tarak