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:
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 )
The final results are collected in a compressed tar archive for downloading and include:
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 )
Coordinate file to upload: OR paste here the SMILES code :
N.B. PrimaDORAC default behaviour [ Do nothing;
Molecule is OK as is ] assumes that the end-user strictly
follows the interface rules; In this dropdown menu, the
interface allows the end-user to switch, at his/her own risk, to non
default behaviour by OpenBabel-checking/adding/removig
hydrogen atoms