AMBER Archive (2005)

Subject: AMBER: Controlling number of water residues...

From: Pavan G (pavanamber_at_gmail.com)
Date: Tue Mar 01 2005 - 01:14:51 CST

Hi

I am trying to build a system of a protein surrounded by a pre-defined
number of water residues. However, when I solvated the protein using
the solvatebox command the number of water residues added far exceeded
the desired number.

I have tried to perform MD on a system of a protein surrounded by 10
boxes each containing 210 water residues ( which is obtained by
solvating a water molecule) with the idea that periodic boundary
conditions will take care of the obvious problem in which water
residues fly off. The 10 boxes were placed randomly. However, the
system was fine till minimization was over but on running MD (sander),
it gave no output, both the .out and .mdcrd files were empty. I
suspect that large empty (vaccum) spaces around the boxes might have
led to instabilities.

Please let me know what the problem is and suggest an appropriate solution.

Pavan Ghatty
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