FAQ


1. How to get started?
Right now, the server is not open to public yet. First, you need to get a valid passphrase. Second, you need to prepare a pdb/mol2 structure file for your molecule. Third, fill the form of parameterization. All necessary fields are rendered in blue. You can use default values for other options. Please refesh your web page everytime to override the cached page when you visit the pages for parameterization since our papges may be updated.

2. Is there any limit for the pdb/mol2 file supplied by users?
All hydrogen atoms must be present and the geometry should be not too bad, e.g., bond lengths are reasonable. The molecule should be not too big, e.g., less than 80 atoms. Since we use other FF, such as CGenFF and GAFF, as the initial parameters. Some atoms or ions are not supported yet by the automated procedure.

3. How long time the parameterization for my molecule will take?
This totally depends on the number of heavy atoms in your molecule and those options you choose as well as the load of our server. The torsion fitting and drude model parameterization could be expensive. Please contact the administrator if you haven't received an email about your parameterization for a non-big molecule (e.g, smaller than 50 atoms and less than 8 soft dihedrals) after several days.

4. What is the objective function used in the parameterization?
The objective function is described detailedly in our paper.

5. What are those files received in my email?
The link of a packed file named as result.tgz is attached if the parameterization is completed successfully. The results for non-polarizable force field parameterization are located under ./result/. The results for a drude force field parameterization are located under ./drude-result/. "readme.txt" describes the files attached.

6. How to set up the equivalent atoms?
If you want to set up the equivalent atoms, you have to provide a FULL list. If "Definition of atom equivalency" is empty, equivalent atoms are detected by the algorithm built in Antechamber.

7. How to choose QM method and basis set?
This would depend on the size and net charge of the molecule and the time you would like to wait for results. The time of parameterization can NOT exceed maximum walltime. About basis set, 6-31G* may be generally reasonable for neutral compounds and cations. 6-31+G* is suggested for anions.



Designed by Lei Huang.