We here provide examples in the form of input PDB files, resulting potential files and exclusion lists to generate a correct potential file usable with polarizable embedding in DALTON.
We include three PDB files, each with a single lipid: POPC, POPS or DMPC. Based on these PDB files we have generated potential files (.pot) to be used in polarizable embedding calculations. In order to correctly account for polarization effects proper exclusion lists have to be generated. The exclusion lists for the PDB files are listed in the bottom of the potential files.
In order to correctly generate the exclusion lists for a different order of atoms we have provided named atom lists (.txt files).
This Figshare project is for the work at the DOI: 10.1002/jcc.24718
|Dato for tilgængelighed||26 jan. 2017|
|Dato for datafremstilling||2015 - 2017|