Introduction

CHARMM-GUI (https://www.charmm-gui.org) is a free web-based platform dedicated to providing powerful tools and resources for molecular simulation research. It is named after "CHARMM" (Chemistry at HARvard Macromolecular Mechanics), a widely used molecular dynamics simulation software. easily construct and simulate complex molecular systems, especially biomolecules such as proteins, lipids, nucleic acids, and their complexes.

Key Features

CHARMM-GUI offers a variety of modules, each targeting different research needs. The following are some of the core functions:

1. molecular modeling: Users can build molecular systems from scratch or upload existing molecular structures (e.g., proteins, DNA, RNA, etc.) and the platform will automatically optimize the structure and add missing atoms.
2. Membrane system construction: For scientists studying cell membranes or lipid bilayers, CHARMM-GUI provides specialized tools to construct complex membrane systems, including protein-membrane complexes.
3. Solution system construction: Users can simulate the behavior of molecules in aqueous or other solvents, and the platform automatically adds solvent molecules and ions to simulate the real environment.
4. Input file generation: CHARMM-GUI can generate input files for a variety of molecular dynamics software (e.g., CHARMM, NAMD, GROMACS, AMBER, etc.), making it easy for users to run simulations directly.
5. Tutorials and Documentation: The platform provides detailed tutorials and documentation to help novices get started quickly, as well as in-depth technical support for advanced users.

Why is it important?Molecular simulation is an important tool for studying the structure and function of biomolecules, but building a simulation system is often very complex and requires a lot of time and expertise. CHARMM-GUI greatly lowers this threshold through automation and a user-friendly interface. Whether you are studying how proteins interact with drugs or exploring the physical properties of cell membranes, CHARMM-GUI provides powerful support.

Who is using it?CHARMM-GUI is widely used by biophysicists, chemists, drug developers and students worldwide. Its user community includes both academic researchers and industrial scientists, especially in the fields of drug design, structural biology, and materials science.CHARMM-GUI is a powerful and easy-to-use tool for molecular simulation research, helping scientists to explore the mysteries of the molecular world more efficiently.

Platform Registration

We open the registration address: https://www.charmm-gui.org/?doc=register as shown below:We have to use foreign edu mailbox, preferably the United States edu, do not use educn will prompt manual review, may be the probability of not receiving charmm-gui verification mail.

name: (First & last name. Example: Wonpil Im) Name: (Surname & first name. Example: Wonpil Im)

Affiliation (Current affiliation. Example: Lehigh University) Affiliation (Current affiliation. Example: Lehigh University)

E-Mail (Current affiliation email only. NO email from qq.com, 163.com, yahoo.com, gmail.com, etc.) Email (Current affiliation email only. NO email from qq.com, 163.com, yahoo.com, gmail.com, etc.) E-Mail (Current affiliation email only. NO email from qq.com, 163.com, yahoo.com, gmail.com, etc.)

After we enter and click submit, we are prompted as shown below:

An email was just sent to you for your email address validation. If necessary, please check your JUNK or SPAM mailbox. If you did not receive our email, you If you did not receive our email, you typed an invalid or wrong email address. If you do not validate your email within 2 days, you need to do the registration from the beginning.

An email has just been sent to you asking you to verify your email address. If necessary, please check your spam or junk mailbox. If you did not receive an e-mail from us, you entered an invalid or incorrect e-mail address. If you do not verify your email within 2 days, you will need to start your registration from the beginning.

We opened our edu mailbox and received the headline:[CGUI email validation]The email is shown below:

Please click here Alternatively, copy the following URL into your address bar.

https://www.charmm-gui.org/?doc=register&do=exist&email=Tim.89128@xxx.edu&passcode=CxSUjhNiQXHR

case of failure

If we fill out personal information that does not meet the CHARMM-GUI requirements, the header of the email we receive is [CGUI User declined]

Your request is declined due to one or more of the following reasons: Your request is declined due to one or more of the following reasons:
1. The name should be your full (first and last) name. 1. The name should be your full name (first and last).
2. Your email should be your affiliation email. 2. Your email should be your affiliation email.
3. The affiliation name should be your affiliation name.3. The affiliation name should be your affiliation name.
4. Your affiliation does not belong to academic and governmental institutes. 4.
Please request your account again with proper information, or get a proper license for commercial use.
The CHARMM-GUI Development Team.

Success Stories

If we fill in the edu email address and personal information to meet the requirements, the title of the email is[CGUI User approved] 

You can now access to the CHARMM-GUI Input Generator modules. Here is your account information.

You now have access to the CHARMM-GUI Input Generator module. Below is your account information:

You can change your information after you login. We recommend that you change your password in 'User Profile' below We recommend that you change your password in 'User Profile' below 'Logout' as soon as possible. We recommend that you change your password in 'User Profile' below 'Logout' as soon as possible.

Here are several tips that can be very useful to resolve a lot of your CHARMM-GUI errors.
(1) 99% CHARMM-GUI errors occur during PDB reading. Please check the following FAQ to resolve common errors. https://charmm-gui.org/faq#pdb_errors.
(2) Regardless of using AMBER or CHARMM FF, the best video demos for Membrane Builder might be.
https://www.youtube.com/watch?v=BUIAG1vHT9c&t=13s and https://www.youtube.com/watch?v=j-KmfDy3vxo&t=16s.
(3) Please check the following FAQs for proper ligand molecule reading and parameterization.
https://www.charmm-gui.org/faq#reading_ligands
https://www.charmm-gui.org/faq#ligandrm_cgenff
(4) Your JOB IDs (less than a week old) are available in your User Profile. CHARMM-GUI only keeps your job(s) for a week.
(5) To get an update and an important notice quickly, please follow CHARMM-GUI on Twitter (https://twitter.com/CharmmGui) and YouTube (https://www.youtube.com/channel/UCtHN7aNAjDet_JKWPxSioLQ).

Thank you!
The CHARMM-GUI Development Team