I.e. don't worry about dimensions, since they will shrink anyway when
you equilibrate. Getting the number of waters to match is the goal.
Bill
On 9/21/17 12:58 PM, Bill Ross wrote:
> 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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>>> AMBER mailing list
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>>>
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Received on Thu Sep 21 2017 - 13:00:09 PDT
