On Sat, Aug 24, 2024, Natesan Mani via AMBER wrote:
>I have been trying to solvate my system using leap and I'm having issues
>with the placement of the periodic box. The waterbox is being placed
>correctly, however, the periodic box is being shifted. The protein is
>centered to origin prior to solvation. The script I used is as follows:
>source leaprc.protein.ff14SB
>source leaprc.water.tip3p
>source leaprc.GLYCAM_06j-1
>complex = loadpdb centered_complex.pdb
>solvatebox complex TIP3PBOX 20
>savepdb complex complex_solv.pdb
>
>I have also attached an image of my system. Could you please help me out?
I'm not sure where the outline of the periodic box came from. But, if it
makes a difference to you, you can use "set default nocenter on" at the
beginning of your tleap script, so prevent the protein (or other solute)
from being translated from its initial position.
(Type "help set_default" inside tleap to see other preferences than can be
set.)
...dac
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Received on Sat Aug 24 2024 - 19:00:02 PDT
