Re: [AMBER] peptide bond restraints

From: lucrecia bogado <>
Date: Thu, 19 Jul 2018 22:50:14 +0000

thanks for your answer,

I will consider your suggestions.To the ligand we add the respective hydrogens,
leaving the final structure as the pdb that I am attaching now.
The amidic bond should not rotate for what we consider to be an error.

De: David A Case <>
Enviado: jueves, 19 de julio de 2018 09:53:37
Para: AMBER Mailing List
Asunto: Re: [AMBER] peptide bond restraints

On Wed, Jul 18, 2018, lucrecia bogado wrote:

> problem that I have is that I
> have been running production MD simulation of enzyme with a ligand by
> Amber14 with ff14sb force field for the protein and Gaff for the ligand,
> in periodic water box, but amidic bond or peptide bond (CO-NH) of the
> ligand rotates during the dynamics, I would like to know how can I
> solution this problem because in the manual user doesn t explain about
> restraints for the ligand, like its my case.

First, are you sure it is a problem? You can force the amide bond to
stay at a given value (see below), but you need to be sure that doing
that doesn't lead to a situation where you just get out what you put in.

Torsion restraints are lumped in with "NMR restraints" in Amber-lingo.
These were historically first used in NMR refinment problems, but need
have nothing to do with NMR; and they don't care if they are being
applied to protein residues or to ligands.

See Section 25.1, "Distance, angle and torsional restraints" in the
Amber 2018 Reference Manual.

Note: you lig.pdb file doesn't have any hydrogens. How did you create
the mol2/frcmod files for the ligand? Check your files to see if the
amide bond in the ligand is assigned atom types appropriate for an amide
bond. You can also use parmed to see what the torsion potential about
that bond is: maybe it is somehow getting treated as a single bond(?)

...good luck....dac

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Received on Thu Jul 19 2018 - 16:00:03 PDT
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