AMBER Archive (2009)

Subject: [AMBER] Leap Questions...

From: Cihan Aydin (cihan.aydin_at_umassmed.edu)
Date: Sat Jul 04 2009 - 20:41:39 CDT

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_at_umassmed.edu
+1 (508) 856-3430

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