Great question! In this essay/short story, "Third Thoughts," this quote is cryptic but there is a clue earlier in the story that helps define what magnatism means. Notice that Lucas spells it magnAtism. This might be an old derivation of how to spell magnetism, but I think it is a reference to the word "magnate" which he uses in the previous line:
City magnates are successful probably just because they don't do these foolish impulsive things.
A magnate can mean a great, noble man or one who is "great" because of wealth. Clearly, the narrator is equating magnate with wealth and/or the ability to be a successful dealer. The "impulse" is to be generous. So, the impulse to be generous negates his "magnatism." In other words, the impulse to be generous negates his ability to be a magnate: a wealthy, successful dealer. If he always acts on his generous impulses, he will never acquire a lot of wealth (become a magnate).
If you want to stretch the definition to include a pun on magnEtism (I've capitalized the letters in bold so you - and I - notice the distinction), you could also say that the generous impulse negates his ability to "attract" future wealth and a successful business, with "attraction" being a pun on magnetic attraction.