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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Received on Thu Sep 21 2017 - 13:00:06 PDT
