AMBER Archive (2008)

Subject: Re: AMBER: impropers over bonds between sidechains

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Wed Aug 20 2008 - 12:14:03 CDT

On Fri, Aug 15, 2008, Grange Hermitage wrote:
>
> They are only immaterial if leap ignores impropers in prepin and refers to
> the force field to build suitable impropers. This was apparently the case 3
> years ago. I am checking that this is still the case. If it is so, I expect
> the same impropers will be built over the sidechain transamide bond as are
> built over the mainchain amide bonds.

Leap will build its own impropers, as it has for two decades. But you
should use the rdparm program to examine your prmtop file, in order to
make sure that you are getting the impropers you want.

...dac

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