The PrimaDORAC web interface is designed to upload a
file, inputmol.ext (allowed file extensions are those
recongnized by Openbabel ),
containing the structure of an organic molecule or a small molecule
drug, eventually producing the primadocarc archive
(thereinafter indicated as PA) that includes the following files:
Piero Procacci, Journal of Chemical Information and Modeling (2017), 57 (6), 1240-1245.
(DOI: 10.1021/acs.jcim.7b0014 )
Values of the AM1/BCC charges in the inputmol.tpg file are in electrons.
- inputmol-p.tpg the topology file of your inputmol.ext file with gaff2016 assignment and AMI-BCC charges
- inputmol-p.prm the parameters file gaff2016 based in ORAC format.
- inputmol-p.pdb pdb file (MOPAC7 minimized coordinates
or original coordinates in case MOPAC7 fails ) with unique labels
matching the .tpg labels.
- inputmol-min-p.pdb pdb file (ORAC/gaff2016 minimized coordinates) with unique labels matching the .tpg labels.
- inputmol-p.log the log file with chemical information for assignment of atomic types. This file contains the chemical information that has been used for the assignment of the atomic types.
- inputmol-p.frq.xyz Vibrational frequencies in vacuo computed with ORAC and GAFF2016 (this file can be viewed with jmol )
- inputmol-p.IR.jpg InfraRed spectrum in vacuo computed with GAFF2016/ORAC.
Units in the inputmol.prm file are kcal/mol, Angstroem and radiants.
Conversion of the .tpg and .prm files to other formats (e.g. amber, gromacs, charmm etc) is straightforward. Refer to orac manual for more info on the parameter and topology files.
The PA is provided in the hope that it is useful but there is no warranty for the information provided therein as formally expressed below. The primaDORAC web interface is conceived to ease some painful and error-prone steps preceding a molecular dynamics simulation involving organic molecules of pharmacological interest. The alert and scrupulous researcher should not take this archive for granted and should carfully go over the primadorac/gaff assignment ( file inputmol-min-p.log ) and check the consistency of the minimized structure based on primadorac assignment ( file inputmol-min-p.pdb ) with the MOPAC7-minimized and/or riginal end-user data
( file inputmol-p.pdb ). PrimaDORAC can be acknowledged by citing the paper:
1. THERE IS NO WARRANTY FOR THE INFORMATION PROVIDED IN THIS PRIMADORAC ARCHIVE (PA), TO THE EXTENT PERMITTED BY APPLICABLE LAW. THIS PA IS PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF INFORMATION PROVIDED IN THIS PA IS WITH YOU AND YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
2. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW WILL THE PRIMADORAC COPYRIGHT HOLDER, OR ANY BODY OF THE FLORENCE UNIVERSITY DISTRIBUTING THIS PA, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE PRIMADORAC AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE PRIMADORAC (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF ORAC TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.