Re: [AMBER] Using amber19sb forcefield to simulate cyclic peptide

From: Carlos Simmerling via AMBER <>
Date: Fri, 17 Feb 2023 19:30:12 -0500

When you say it is cyclic, how is the connection made? Is the backbone
circular, or a crosslink with disulfide or similar? What are the details of
the terminal residues?
Let me know and we can help you get this working. Should be

On Fri, Feb 17, 2023, 5:56 PM Ho, Minh via AMBER <> wrote:

> Hello,
> I want to simulate a cyclic peptide with sequence (ALA-ALA-ALA-ALA-ALA)
> using amber19sb forcefield. All the amino acids are in L- form. I have
> prepared a .pdb file that I can use to generate a .parm7 and a .crd file
> for this cyclic peptide. However, the CMAP entries are missing for the
> terminal residues. Based on Amber20 manual, I have noticed that CMAP will
> not be applied to terminal residues. I can circumvent this issue by
> manually modifying .parm7 file. I would love to know if there is a way to
> force tleap to assign CMAP to "terminal" residues of cyclic peptide?
> Thank you
> Minh
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Received on Fri Feb 17 2023 - 17:00:03 PST
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