Hello EMC users, is it possible to remove hydrogen atom from some atoms
any help will be highly appreciated
Dear User,
I will try to answer your question, while not knowing what exactly you are trying to accomplish. EMC follows the standard Daylight SMILES definition, in which hydrogen completion is applied according to standard rules. Extra hydrogens can be added by explicitly adding them to your SMILES. Take for instance neutral pyridine, which has c1ccccn1 as SMILES. The protonated form would be accomplished with c1ccccn1H. Protonated ethyl amine is represented by either CC[N+] or CCN(H)(H)H.
thank you so much for your reply, actually i want to prepare pre and post reaction template for bond/react commands in lammps, so in my file i needed carbon atom without hydrogen atom, but EMC added hydrogen atom automatically, i want how to prevent addition of hydrogen atom on my edge atom
thank you
You could control the number of hydrogens by using [C-], [C–], etc. Another alternative is the use of radicals in the form of [C.]. The latter is currently not supported. The problem with both solutions is, that your force field would have to support these type of moieties, i.e. it would need to have rules for [C-] or [C.].
noted, thank you so much, i will try it