I think the best solution in amber is to use solvatebox iteratively
varying params until you get just a few more waters than you want, then
delete a few manually in xleap.
Outside of amber, maybe packmol can do it.
Bill
On 9/21/17 12:55 PM, Ashutosh Shandilya wrote:
> Thanks for your reply, I want to make several systems of same protein (with
> different configuration) with equal number of water molecules. I took the
> largest water box and calculated its dimension and followed by set of
> commands mentioned above.
> *Solvatebox* command makes waterbox which has different number of water
> atoms for same proteins with different conformation. So If I use "*solvatebox
> mol TIP3PBOX 10.0"* it gives different number of water molecules with
> different conformation of protein.
>
> Thats why I want to use setbox command or somehow I can fix the dimension
> of waterbox to have same number of water molecule around the protein. Some
> online suggestion and manual suggested to "*setbox* var vdw or center"
> which should automatically fill water molecules.
>
> Any suggestion in forming waterbox with fix dimension would help.
>
> Many thanks
>
>
> On Thu, Sep 21, 2017 at 3:46 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> On Thu, Sep 21, 2017 at 12:13 PM, Ashutosh Shandilya
>> <scfbioiitd.gmail.com> wrote:
>>> It saves pdb but with no water. I also tried other options such as
>>> solvatebox var {xx xx xx}. This didn't work as well. Few on line search
>> and
>>> manual suggested using
>> The 'solvatebox' and 'solvateoct' commands in tleap are the only
>> commands that will both create a unit cell and fill it with solvent.
>> Can you describe in more detail what you did when you tried
>> 'solvatebox', and why it didn't work for you?
>>
>> -Dan
>>
>> --
>> -------------------------
>> Daniel R. Roe
>> Laboratory of Computational Biology
>> National Institutes of Health, NHLBI
>> 5635 Fishers Ln, Rm T900
>> Rockville MD, 20852
>> https://www.lobos.nih.gov/lcb
>>
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>>
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Received on Thu Sep 21 2017 - 13:00:07 PDT
