Greetings Amber Commnity,
I have a leap-specific question. When I solvate my molecule with
solvateOct, the water box is situated very near to the boundary of the
truncated octahedron. That's not the case when I solvate in a normal
box. So is there any way to avoid this? All the proteins are solvated
with a 10.0A cutoff for the nearest solute residue. I am attaching the
PDB's for comparison (bzipped to fit in the message).
Another question is - Is there a way to keep track of the crystal
waters? LEaP loads them as solute so their identity gets lost.
--
Cihan Aydin
UMass Graduate School of Biomedical Sciences
PhD Student . Schiffer Lab
364 Plantation St. LRB 970M
Worcester, MA 01605
cihan.aydin.umassmed.edu
+1 (508) 856-3430
Received on Mon Jul 06 2009 - 17:28:55 PDT
