AMBER Archive (2008)

Subject: Re: AMBER: impropers over bonds between sidechains

From: Grange Hermitage (ghermitage_at_gmail.com)
Date: Thu Aug 14 2008 - 22:08:49 CDT

Hi Bud,

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.

cheers,
   John.

On Fri, Aug 15, 2008 at 11:59 AM, M. L. Dodson <
activesitedynamics_at_comcast.net> wrote:

> On Fri, Aug 15, 2008 at 10:42:05AM +0930, Grange Hermitage wrote:
> > Hi,
> >
> > I have caps on sidechains to handle a bond being formed between a LYS and
> > ASP derivative new residues.
> > These new residues are charge fitted by RESP on Gaussian output.
> > When prepgen generates a prepin file for each of these new residues,
> > impropers are generated for what will be the amide bond between the LYS
> and
> > ASP derivative residues. However, the atoms of the sidechain caps will be
> > removed and impropers referring to the removed atoms presumably lost. How
> to
> > specify an improper that refers to atoms of two residues? (the residues
> are
> > not adjacent in the sequence).
> >
> > I see in a send some years ago that impropers in a prepin are ignored by
> > leap.
> > Is this still the case?
> > If so, the problem of how to specify in prepin an improper over atoms of
> two
> > sidegroups is immaterial.
> >
> > cheers,
> > John.
>
> How about just deleting the ones that are immaterial?
>
> Bud Dodson
> --
> M. L. Dodson
> Business Email: activesitedynamics-at-comcast-dot-net
> Personal Email: mldodson-at-comcast-dot-net
> Phone: eight_three_two-56_three-386_one
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