AMBER Archive (2004)

Subject: AMBER: undefined loops and protonate

From: Stern, Julie (
Date: Thu Mar 25 2004 - 11:52:41 CST

Hello Amber-ites,
    I have two undefined loops in my pdb file. The undefined
loop regions originated from little or nothing appearing in
electron density maps indicating a region of large flexibility.
    First I tried treating the molecule as separate chains which
resulted in 'atoms moving too fast - simulation is unstable.'
Then I tried to input coordinates to define the loops with the
intent of setting the occupancy column in the pdb file to a
low value. When I used protonate, not only was the occupancy
column removed but so was the temperature column. Temperature
gets put back in from my namd configuration file, but occupancy
does not.
     Does anyone have any more suggestions on the handling of
undefined loops? How do I use protonate and keep the occupancy

     Thanks for any help and info.

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