AMBER Archive (2009)

Subject: Re: [AMBER] Disappearing common atoms in Amber 10 with TI

From: case (case_at_biomaps.rutgers.edu)
Date: Fri Jul 17 2009 - 06:41:39 CDT

On Thu, Jul 16, 2009, Khavrutskii, Ilja wrote:

> What would be the best way to ensure that vc-vh bonds are SHAKEn?

I think you want the opposite: use the noshakemask to ensure that the
corresponding real c-h bonds are *not* shaken.

I really recommend using softcores instead for this sort of thing. First, as
you have found, you have to be very careful in setting up dummy atoms, and you
do have to make sure that everything is completely compatible between the two
endpoints. Amber doesn't check for everything that could go wrong. Plus, as
Thomas as pointed out, getting good convergence without the softcore option is
a tricky business in itself.

...dac

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