Number of residue types is greater than MAX_RESIDUE_TYPES. Rerun with -override_rsd_type_limit. Or if you have introduced a bunch of patches, consider declaring only the ones you want to use at the top of your app (with the options) with the command option[ chemical::include_patches ].push_back( ... ). 
ERROR:: Exit from: src/core/pack/task/ResfileReader.cc line: 1520
terminate called after throwing an instance of 'utility::EXCN_utility_exit'
/cm/local/apps/sge/current/default/spool/node-088/job_scripts/4647743: line 20: 14505 Aborted                 ddg_monomer.linuxgccrelease @ /home/ucbechz/Scratch/20141212_ddg_renumber/1A/input/options > ddg.log
tar: Removing leading `/' from member names