[AMBER] Using amber19sb forcefield to simulate cyclic peptide

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From: Ho, Minh via AMBER <amber.ambermd.org>
Date: Fri, 17 Feb 2023 22:56:18 +0000

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 - 15:00:03 PST