AMBER Archive (2009)

Subject: Re: [AMBER] Regarding rigid bond

From: case (case_at_biomaps.rutgers.edu)
Date: Tue Dec 01 2009 - 06:50:15 CST

On Tue, Dec 01, 2009, Carlos Simmerling wrote:

> the only option is to constrain all bonds. you cannot do this for some bonds
> and not for others unless you modify the code (which is not possible unless
> you have programming experience).

There is the "noshakemask" option that might help: you would turn on SHAKE,
then turn it off for the parts where you don't want it. Check carefully that
you are getting what you really want.

....dac

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