Mark J. Williamson created
Please see the link: http://ambermd.org/formats.html#parm.dat This explains the format used in the file. With respect to the terms that you describe as "duplicate atom groups with different params", a single given torsion parameter can be synthesised from multiple cosine terms ( see p259 of http://ambermd.org/doc8/amber8.pdf ) and the use of the negative PN value is an indication NOTE: If PN .lt. 0.0 then the torsional potential is assumed to have more than one term, and the values of the rest of the terms are read from the next cards until a positive PN is encountered. The negative value of pn is used only for identifying the existence of the next term and only the absolute value of PN is kept.