-I: Adding /opt/amber16/dat/leap/prep to search path.
-I: Adding /opt/amber16/dat/leap/lib to search path.
-I: Adding /opt/amber16/dat/leap/parm to search path.
-I: Adding /opt/amber16/dat/leap/cmd to search path.
-f: Source /home/local/soemya-loc/site_1_WT/MD_am1/ZINC01482113/cryst/leap_script_1.in.

Welcome to LEaP!
(no leaprc in search path)
Sourcing: /home/local/soemya-loc/site_1_WT/MD_am1/ZINC01482113/cryst/leap_script_1.in
----- Source: /opt/amber16/dat/leap/cmd/oldff/leaprc.ff99SB
----- Source of /opt/amber16/dat/leap/cmd/oldff/leaprc.ff99SB done
Log file: ./leap.log
Loading parameters: /opt/amber16/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99
Loading parameters: /opt/amber16/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
Loading library: /opt/amber16/dat/leap/lib/all_nucleic94.lib
Loading library: /opt/amber16/dat/leap/lib/all_amino94.lib
Loading library: /opt/amber16/dat/leap/lib/all_aminoct94.lib
Loading library: /opt/amber16/dat/leap/lib/all_aminont94.lib
Loading library: /opt/amber16/dat/leap/lib/ions94.lib
Loading library: /opt/amber16/dat/leap/lib/solvents.lib
----- Source: /opt/amber16/dat/leap/cmd/leaprc.gaff
----- Source of /opt/amber16/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /opt/amber16/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.8, Mar 2015)
Loading library: /home/local/soemya-loc/site_1_WT/leap/ZINC01482113/ZINC01482113_am1.lib
File: /home/local/soemya-loc/site_1_WT/CA.lib is not a valid database.
Loading PDB file: /home/local/soemya-loc/site_1_WT/leap/ZINC01482113/ZINC01482113_lig.pdb
Error: Atom .R<<1> 1>.A<C5 7> has force field coordination 4
       but only 3 bonded neighbors.
       The cause may be an incorrect atom type, and
       the effect may be a crash very soon.
Error: Atom .R<<1> 1>.A<O3 8> has force field coordination 2
       but only 1 bonded neighbors.
       The cause may be an incorrect atom type, and
       the effect may be a crash very soon.
/opt/amber16/bin/tleap: line 17: 13678 Segmentation fault      $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep -I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd $*