Welcome to the PrimaDORAC web interface

Dept. of Chemistry, University of Florence

PrimaDORAC is a simple web interface that reads the coordinates of an organic molecule (no more than 60 heavy atoms) and produces the topology and parameters files for molecular dynamics simulations.

PrimaDORAC uses mopac7 for producing AM1-BCC charges and gaff2016 atomic types for topology definition. Prior to uploading or entering the SMILES string, read the README file and mind these few rules:

• Allowed file format/extensions are all Openbabel supported format specifications ( .sdf , .pdb, .mdl , .mol2 , .xyz , .gau )
• input file may contain only H C N O S P F Cl Br I atoms. Use only standard atomic symbols in the inputfile.
• input file must contain only one molecule at a time.
• no ",\()=#~:;" characters are allowed in the filename to upload; dash "-" and plus "+" characters can be used (see below)
• If the molecule is charged, the total charge must be specified in the filename using the two characters before the extension (e.g. acetic-adid-1.sdf ammonium+1.sdf )
• When the charge is specified in the name (+/-), the molecule must contains all atoms, including hydrogen atoms (these can be attached using, e.g., babel -h mol-noh.pdb mol-h.pdb )

• inputmol-p.tpg the topology file with gaff2016 assignment and AMI-BCC charges
• inputmol-p.prm the gaff2016-based parameters file
• inputmol-p.log log file with chemical information for assignment of atomic types.
• inputmol-p.pdb pdb file (original coordinates) with unique labels matching the .tpg labels.
• inputmol-min-p.pdb pdb file (gaff2016 minimization) with unique labels matching the .tpg labels.
• inputmol-p.frq.xyz Vibrational frequencies in vacuo computed with ORAC (this file can be viewed with jmol )
• inputmol-IR-p.jpg computed InfraRed spectrum using GAFF2/PrimaDORAC parameters
• inputmol-g.top inputmol-g.itp inputmol-g.mdp Topology/itp files for GROMACS addicted (no warranty!)