AMBER Archive (2004)

Subject: Re: AMBER: undefined loops and protonate

From: David A. Case (
Date: Thu Mar 25 2004 - 18:37:47 CST

On Thu, Mar 25, 2004, Stern, Julie wrote:

> 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.

Amber neither reads nor uses the occupancy column. Your best bet is probably
to use a homology modeling program (SwissProt, Modeller, others come to mind)
to build likely coordinates for the missing loops, before starting up with

Note also that protonate is really only necessary in special circumstances;
in most cases the proton positions that LEaP automatically generates should
be fine as a starting point for simulations.

...good luck...dac


================================================================== David A. Case | e-mail: Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to