AMBER Archive (2004)

Subject: AMBER: questions regarding JTREE

From: Annette Höglund (
Date: Wed Oct 27 2004 - 10:37:06 CDT

Dear All,

I use ntr=1 and if I want to fix the solute in water I can do:

Fix the molecule
RES 1 108

How can I fix the solute except its hydrogen atoms (without enumerating
all atom types (JGRAPH)).
I guess the JTREE is what I should go for, but the manual isn't very
helpful at this point...
What does M, S, B, 3, E mean for a) proteins, b) DNA?

What is the difference between ntr and ibelly? And when should I prefer

Thanks in advance!


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