Re: Xtal Waters and SolvateBox

From: Michael Cooney <>
Date: Mon 30 Oct 2000 14:52:32 -0500 (EST)

Dear Dr. De Las Rivas,
I have just recently begun using xLEAP myself, and the only
suggestion that I would make is to check the output PDB file
from LEAP (you will need to use carnal or pdbgen to create this from the
inpcrd file) to see if the crystal waters are part of the solute or of the
solvent. My suggestion would be to add a "TER" on a line by itself _after_
the crystal waters, not before; the solvent waters should follow this
"TER", and an "END" statement (again on its own line) should close the PDB
file. After modifying the solvated PDB file, you can try reading it
back into xLEAP, get a new .crd file, and use this for SANDER
Good luck!

Michael G. Cooney
Department of Biochemistry and Molecular Biology
The University of Georgia
Athens, GA 30602
Received on Mon Oct 30 2000 - 11:52:32 PST
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