Re: [AMBER] Preparing/generating input files for Amber MD

From: Carlos Simmerling <>
Date: Mon, 1 Nov 2021 15:50:48 -0400

you might want to check out CHARMM-GUI (it builds Amber systems as well).

On Mon, Nov 1, 2021 at 3:32 PM Jhuma Das <> wrote:

> Hello!
> I am wondering if there is a GUI interface or a more automated way to
> build the protein-ligand or protein-DNA MD system that will go through
> various steps starting from PDB structure, clean up/add missing
> loops/disulfide formation, solvation, neutralization of the system, adding
> salt, and generate relevant complex topology files (e.g., some Knime
> workflow).
> If not, can a solvated protein-ligand/protein-DNA system from Maestro be
> used to generate the input topology and coordinate files using LeaP program
> for running Amber simulations?
> Best regards,
> Jhuma
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Received on Mon Nov 01 2021 - 13:00:03 PDT
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