Help

Thermodynamic Integration with Enhanced Sampling -
  Displayed Stages:
  1) Upload files,
  2) Merge ligands,
  3) Download .zip and check the log,
  5) Simulate MD,
  6) Analyse the results.

Below are some commonly asked questions which may be able to help solve your problem. If you're still having troubles please contact us on contact@ccs-ties.org.

.mol2 files preferrably with GAFF

At the moment we encourage using .mol2 files with charges assigned (GAFF).

Whereas .pdb files will work, they require AM1-BCC charges to be assigned which is computationally expensive for us.

Go to our ligands page to upload your files or select files you have already uploaded.

As many as you want

You can upload as many ligand files as you want and they will be available on the ligands page to select at any time.

However, at the moment, you will only be able to run two ligand files through TIES at a time. In the future we are planning to increase functionality to allow for more ligands to be analysed at once.

Read our publication

For more information about the TIES software you can read our recently published the paper "TIES 20: Relative Binding Free Energy with a Flexible Superimposition Algorithm and Partial Ring Morphing" in the JCTC.

Feel free to contact us if you have a specific question, and please note that we are hoping to expand our WebTIES service.

Yes!

The software had initially been made free to use for anyone with an academic email address.

However, we are working on making our software more accessible.

Anyone with an academic email address

Anyone with an academic email address can use TIES and have their account activated automatically.

Users without an academic email will have their account activated manually (please email contact@ccs-ties.org).

No

However, we reserve the right to access files if an error in the software occurs, allowing us to improve our service.

Yes

Removing the ligand completely deletes the file and all associated metadata.

Yes

The initial WebTIES release can fail for different reasons. The generated failed zip will contain the log (ties.log) as well as all files that can help in debugging the issue. We are happy to assist you at contact@ccs-ties.org.

  1. Go to ligands and generate the hybrids .zip files. Check the ties.log file for more information.
  2. Simulate the hybrids with the ties_md package with support for NAMD or OpenMM
  3. Analyse the results with ties_ana

For a higher throughput, yes. However, a small set of GPUs can perform very well. We are currently not making our resources available for the computationally heavy part of running molecular dynamics simulations.


Clicky