Dear Lee Cato,
This is a guess, but it is possible that the generated system is so huge that it scapes the PDB format (either number of atoms, residues or coordinates)... hence VMD is misreading the file... alternative it may be placed at the limits of the accepted xyz coordinates in the PDB rendering similar issues...
Have you tried generating the topology and *.ncrst file and checking them in VMD?
Because those file should not have such issues... that could help debugging the leap output...
Best,
MatÃas
------------------------------------
PhD.
Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay
[
http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
[
http://www.sirahff.com]
----- Mensaje original -----
De: "Lee Cato" <michael.lee.cato.emory.edu>
Para: amber.ambermd.org
Enviados: Jueves, 22 de Abril 2021 11:43:46
Asunto: [AMBER] Problem with incomplete solvation with tleap
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 - 09:30:02 PDT
