AMBER Archive (2000)

Subject: Re: question

From: David Case (case_at_scripps.edu)
Date: Tue Nov 07 2000 - 13:55:47 CST

On Tue, Nov 07, 2000, Paola d'Alessio wrote:

> Why do I get the following message in the output file when I try to
> minimize an alpha-helix using the IBELLY option of Sander, version 6.0
>
> When igb>0, the moving part must be at the
> start of the molecule. This does not seem
> to be the case here.

I tried to make this message informative....If there are N "moving" atoms,
they must be the first N atoms in the molecule (when igb>0 as the message
states). You have moving hdyrogens interspersed with non-moving heavy
atoms.

Best suggestion: use sander_classic for this sort of calculation: the
restriction on the belly atoms does not apply there. In general, "vacuum"
simulations (where you might use igb=2 or 3 in sander) will probably run
faster and with fewer limitations if you use sander_classic.

...hope this helps....dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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