Why to use the USER FRAGMENT library to build glycoconjugates in InsightII ?
ANSWER 1- In Accelrys software package, a relation exists between the FRAGMENT libraries (used for building molecules such as oligopeptides or oligonucleotides with the “Biopolymer” module) and the RESIDUE library belonging to a FF (for example, with the CVFF force field, the “cvff.rlb” file is used to match the residue names, the atom names, the partial charges and atom types of the studied molecule). Indeed, the atom names, residue names, rules of linkage between different units are set up in the RESIDUE and FRAGMENT libraries in a way allowing a perfect fit between these two libraries. Thus, an oligopeptide built with the “Biopolymer” module will be automatically recognized by the CVFF force field. 2- The AMBER FF topology database of the amino-acids and nucleotides (“all_amino94.in”, “all_aminont94.in”, “all_aminoct94.in” and “all_nuc94.in” files, for the Cornell et al. FF, for instance) shares similar rules with the corresponding Accelrys FF database (RESIDUE libraries provided by
