PrimadORAC: a free web interface for the assignment of partial charges, chemical topology and bonded parameters in organic or drug molecules

We present PrimaDORAC, a simple and freely accessible web interface for generating the topology and the parameter files of organic or drug molecules, to be used in molecular mechanics or molecular dynamics calculations. The interface relies on our in-house FORTRAN90 parser, working on the recently released Generalized Amber Force Field parameter set (GAFF2). AM1/BCC charges are computed using the Public Domain MOPAC7 program and the bond charge corrections (BCC) reported in Ref. Jakalian et al, J Comp Chem, 2002, 23, 1623-1641. The interface has been tested on about 52000 compounds (identified with a CAS-registry number) taken from the National Cancer Institute (NCI) Open Database. PrimaDORAC has been found very reliable producing GAFF2 minimized structures bearing a mean Root Square Displacement of about 0.01-0.02 nm with respect to the original CORINA generated 3D NCI structures. As a demonstrative example, we release the full topology and parameter files, along with the AM1/BCC-GAFF2 computed <em> in vacuo </em> IR spectrum, for some recently discovered PARP/MCL1 inhibitors. The web interface and parser, including the sources, are part of the ORAC code [Procacci, J. Chem. Inf.