Re: [AMBER] Isopeptide bond Asp-Lys - parameters?

From: FyD <>
Date: Thu, 05 Jun 2014 07:56:03 +0200

Dear Anselm,

> does anyone have parameters (preferably parm99SB) available for an
> isopeptide bond system containing Asp and Lys?

I am not sure specific parameters were generated for an "isopeptide" bond...
My feeling is that you need to generate the corresponding molecular
fragments/force field libraries, and be able to connect them together.

A peptide bond is generally split into two building blocks; each
building block has a capping group (MeCO and NHMe) and a peptide bond...

    R1NH-COR2 <-- R1NH-COMe MeNH-COR2 <-- R1NH COR2 <-- R1NH-COR2

then you set two intra-molecular charge constraints during the charge
fitting step for these capping groups so that you are able to generate
the R1NH and COR2 fragments, which can be associated...

all these process can be automatically done using PyRED at R.E.D. Server Dev.

besides the 2 intra-molecular charge constraints you can also add an
inter-molecular charge constraint between the 2 capping groups and
PyRED will automatically associate the two fragments; i.e. the
molecular fragment association does not need to be done by the LEaP

regards, Francois

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Received on Wed Jun 04 2014 - 23:00:03 PDT
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