I am running into a problem with solvating a complex that I have never seen before.
It looks like only half of the pdb is solvated after issuing the following commands:
source leaprc.protein.ff14SB
source leaprc.GLYCAM_06j-1
source leaprc.water.tip3p
pdb=loadpdb complex.pdb
solvateOct pdb TIP3PBOX 10.0
savepdb pdb solvated_complex.pdb
There is a strange column of water projecting through the middle, and only half of the complex is surrounded by water.
The same image is seen on vmd and pymol. Do you know why this may be occurring? The protein is rather large, but this computer and amber setup (amber20) has worked fine for other protein sims.
Best,
Cato
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Received on Thu Apr 22 2021 - 08:00:03 PDT
