AMBER Archive (2005)

Subject: Re: AMBER: nmode with ibelly

From: David A. Case (case_at_scripps.edu)
Date: Tue Jun 07 2005 - 09:41:41 CDT

On Tue, Jun 07, 2005, Martin Sippel wrote:
>
> ...with ibelly = 1 option the entropy calculation doesn't work
> (there ist this message: "Thermo analysis not supported for belly calc.") ?!
> How can I define that only certrain residues should be considered for the
> entropy calculation to speed it up?
>

You would have to create a prmtop file with just the "important" residues, and
use ptraj to strip away the unwanted parts of the system. Then run what is
left through nmode.

You could also enable the printing of thermodynamic information when belly is
enabled, but be sure to think carefully about what the results mean.

...dac

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