Re: [AMBER] Isopeptide bond parameterization

From: Dr. Anselm Horn <>
Date: Thu, 11 Nov 2021 16:32:21 +0100

Dear Venkat,

some time ago, I generated parameters for an isopeptide bond, i.e.
residues LYX, GLX, and ASX that contain an additional valency like CYX
for cross-linking. I used the approach with blocking groups ACE and NME
and utilized PyRED.

In this way it is possible to build peptides with isopeptide bonds (i.e.
a cross-link between the side chains of LYS, GLU/GLN or ASP/ASN ->
omega-omega-bond) or with alpha-omega bonds (i.e. a link between the
side chain of one residue and the C- or N-terminus of another one). The
parameter set is thus rather versatile.

The respective publication is still about to be submitted, but of course
I'd like to share my work, if you are interested. In that way, please
contact me off the list.

Best regards,


Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)

Am 11.11.2021 um 14:51 schrieb Venkatareddy Dadireddy:
> Dear Amber Users,
> My simulation system contains isopeptide bond between
> lysine and terminal glycine. I want to generate ff parameters for
> isopeptide bond using PyRED. I am following tutorials at
> I am following two approaches (please find the schematic attached).
> Approach 1: Using lysine-glycine isopeptide bonded molecule
> with caps (ACE and NME). During charge fitting, charge constraints
> are applied (MOLECULE1-INTRA-MCC = 0) for ACE, NME, LYS part
> and GLY part and ACE and NME caps are discarded. Library for LYS and GLY parts are
> saved separately (say and and used during system build
> with tleap.
> Approach 2: ff parameters are generated from separate LYS and GLY residues
> with ACE and NME caps and charge constraints are applied as in 'Approach 1'.
> Please help me with the following questions:
> 1. What is the best between the two approaches. If both are wrong, please
> 2. suggest me the right approach.
> 3. How to choose the conformations of an input molecule (.pdb) for PyRED input.
> 4. I have chosen the one that is found in my pdb file.
> 5. What is the best charge model for charge derivation.
> 6. I am using RESP-A1 (HF/6-31G(d)//HF/6-31G(d) ), the default set.
> 7. If anyone has ff parameters available for isopeptide bond,
> 8. I request the same.
> Thank you,
> Venkat
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Received on Thu Nov 11 2021 - 08:00:02 PST
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