The <tt> primadorac </tt> web interface is designed to upload a
file, <tt>inputmol.ext</tt> (allowed file extensions are those
recongnized by <a href="http://openbabel.org/"> Openbabel <a>),
containing the structure of an organic molecule or a small molecule
drug, eventually producing the <b>p</b>rimadocarc <b>a</b>rchive
(thereinafter indicated as PA) that includes the following files:
<ul> 
<li> <tt> inputmol-p.tpg </tt> the topology file of your <tt> inputmol.ext </tt>  file with gaff2016 assignment and AMI-BCC charges
<li> <tt> inputmol-p.prm </tt> the parameters file gaff2016 based in ORAC format.
<li> <tt> inputmol-p.pdb </tt> pdb file (MOPAC7 minimized coordinates
or original coordinates in case MOPAC7 fails ) with unique labels
matching the .tpg labels.
<li> <tt> inputmol-min-p.pdb </tt> pdb file (ORAC/gaff2016 minimized coordinates) with unique labels matching the .tpg labels. 
<li> <tt> inputmol-p.log </tt> 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. 

<li> <tt> inputmol-p.frq </tt> Vibrational frequency <i> in vacuo </i> computed with <a href="http://www.chim.unifi.it/orac"> ORAC </a> and GAFF2016 (this file can be viewed with <a href="http://www.jmol.org">  jmol <a> or <a href="https://avogadro.cc/"> avogadro</a>)  

<li> <tt> inputmol-p.IR.jpg </tt> InfraRed spectrum in vacuo computed with GAFF2016/ORAC.

</ul> 

Values of the AM1/BCC charges in the <tt> inputmol.tpg file </tt> are in electrons.<br>
Units in the <tt> inputmol.prm file </tt> are kcal/mol, Angstroem and radiants.<br>  
Conversion of the <tt> .tpg </tt> and <tt> .prm  </tt> files  to other formats (e.g. <tt> amber, gromacs, charmm </tt>etc) is straightforward. Refer to <a href="http://www.chim.unifi.it/orac/orac-manual.pdf">orac manual</a> for more info on the parameter and topology files. 
<br> 
<br> 
This archive is provided  in the hope that it is useful but there is no warranty for the information provided therein as formally expressed below. The <tt> primadorac </tt> 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 <tt> primadorac/gaff </tt> assignment ( file <tt> inputmol-min-p.log </tt> )  and check the consistency of the minimized structure based on <tt> primadorac </tt> assignment ( file  <tt> inputmol-min-p.pdb </tt> )  with the MOPAC7-minimized and/or riginal end-user data 
( file <tt> inputmol-p.pdb </tt>  ) 
<br>
<br> 

<tt>
NO WARRANTY
</tt> 
<br><br>  
<tt>
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.

</tt>
<br> <br> 

<tt>
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.

</tt>