Re: [AMBER] Problem with Creating Unit for Non-standard N-Cap Residue

From: FyD <>
Date: Tue, 03 Mar 2015 10:31:34 +0100

Dear Tao,

  and its tutorial:

and particularly:

in agreement with:

regards, Francois

> I am doing simulation on system that with various compounds bonded to the
> N-terminal of certain peptide, like shown in the following picture. Now I
> am facing the problems with creating unit for such N-Cap residue.
> ?
> 1. Should I treat R1 combined R' as a N-Cap residue or just the R' only?
> 2. In any case above, is there any method available to assign correct
> partial charge and atom type for such non-standard residue?

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Received on Tue Mar 03 2015 - 02:00:03 PST
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