You can do this:
conf.CreateMap<SourceType, DestinationType>()
.ForSourceMember(x => x.SourceProperty, y => y.Ignore());
Or, in latest version of Automapper, you simply want to tell Automapper to not validate the field
conf.CreateMap<SourceType, DestinationType>()
.ForSourceMember(x => x.SourceProperty, y => y.DoNotValidate());