[AMBER] Preparing/generating input files for Amber MD

From: Jhuma Das <JDas.syros.com>
Date: Mon, 1 Nov 2021 19:32:09 +0000


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,

E-MAIL CONFIDENTIALITY NOTICE: This e-mail message is intended solely for the addressee(s) and may contain confidential and/or legally privileged information. If you are not the intended recipient, or this e-mail was addressed to you in error, you should delete this e-mail message and any attachments, and you are notified that disclosing, copying, distributing or taking action in reliance on the contents of this information is strictly prohibited.
AMBER mailing list
Received on Mon Nov 01 2021 - 13:00:02 PDT
Custom Search