ChemServerQuestions and answers
Everything people usually ask before their first run. Anything missing? Email chris@chemserver.online.
Is ChemServer free?
Yes. Creating an account is free and every account gets 200 MB of storage. There is no paid plan at the moment.
Do I need to install anything?
No. Everything runs on our servers; you only need a web browser. That includes AutoDock Vina, Vina-GPU, GNINA, MGLTools, Meeko, Open Babel, RDKit, PDBFixer and PyMOL.
Which docking programs can I use?
AutoDock Vina 1.2 on CPU, and Vina-GPU 2.1, GNINA 1.3 and Vina-GPU with GNINA CNN rescoring on GPU. Receptors and ligands can be prepared with AutoDock Tools (MGLTools) or Meeko.
How many ligands can I dock in one run?
Up to 50 ligand receptor pairs per run on a free account, for example 50 ligands against one protein or 10 ligands against 5 proteins. Email us if you need larger runs.
How do I get GPU docking?
Choose Vina-GPU or GNINA as the engine. These run on our GPU compute servers; when all of them are busy your run waits in the queue and the page shows when it will start. For regular heavy use, email us to ask for GPU access.
Can I run molecular dynamics or DFT?
Yes, on request. Both are opened per account. Email chris@chemserver.online with your system and what you need. See molecular dynamics and DFT.
Which file formats are supported?
Proteins as PDB (fetched from RCSB by ID or uploaded) and PDBQT. Ligands as SMILES, SDF, MOL, MOL2, PDB, PDBQT, SMI or ZIP archives of PDBQT files. Results come as PDBQT, PDB, SDF, MOL2, Excel workbooks and PNG images.
How long are my files kept?
Results of each run are kept for 90 days. Files you save to Home in My Files are kept with no time limit. Each account has 200 MB in total. Accounts are never deleted automatically.
Can I close the browser while a run is going?
Yes. Runs belong to your account, not to the browser tab. Sign in again later and the results are waiting.
How many runs can I start at once?
One main run per account at a time. Short analyses and image renders can run beside it.
Is my data private?
Your files are visible only to your account in the app and are never shared or published. They are stored on our servers, so check your institution's rules before uploading confidential structures.
How do I cite ChemServer?
Cite the programs your run used (for example AutoDock Vina, Vina-GPU, GNINA, AutoDock Tools or Meeko, RDKit, Open Babel, PDBFixer) and mention ChemServer (https://chemserver.online) in your methods section.
I forgot my password.
Email chris@chemserver.online from the address you registered with and we will send you a new one time password.