On Thu, Sep 21, 2017, Ashutosh Shandilya wrote:
> I am trying to set a water box around a protein with a fix dimension with
> following commands
>
> source leaprc.protein.ff14SB
> source leaprc.water.tip3p
> var = loadpdb a1.pdb
> *set var box {140.1 92.4 93.9} *
> addions2 var Na+ 105 Cl- 95
> savepdb var a.pdb
Use SolvateBox to add waters to a box around a protein. As you found out,
just using the "set" command creates the box, but does not add waters.
If you need a fixed diemsion box, you need to use AddToBox (or a third-party
tool like packmol) to create the solveate system as a pdb file; then load
that into tleap. Since the water is already there, using the "set" command
to tell leap the box size is then the proper thing to do.
...good luck...dac
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Received on Thu Sep 21 2017 - 14:00:02 PDT
