Date: Sat, 24 Aug 2024 17:59:28 +0000
Hello all,
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?
Thanks,
Natesan.
Natesan Mani
(pronouns: he/him)
PhD student,
Department of Chemical Engineering,
Northeastern University.
Phone: +17134017811
Email : mani.na.northeastern.edu
LinkedIn<http://www.linkedin.com/in/natesan-mani> | Website<https://sites.google.com/view/simbiosyslab>
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(image/png attachment: Waterbox.png)
