-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.ff14SB ----- Source of /opt/amber16/dat/leap/cmd/oldff/leaprc.ff14SB done Log file: ./leap.log Loading parameters: /opt/amber16/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA Loading parameters: /opt/amber16/dat/leap/parm/frcmod.ff14SB Reading force field modification type file (frcmod) Reading title: ff14SB protein backbone and sidechain parameters Loading library: /opt/amber16/dat/leap/lib/amino12.lib Loading library: /opt/amber16/dat/leap/lib/aminoct12.lib Loading library: /opt/amber16/dat/leap/lib/aminont12.lib Loading library: /opt/amber16/dat/leap/lib/nucleic12.lib Loading library: /opt/amber16/dat/leap/lib/atomic_ions.lib Loading library: /opt/amber16/dat/leap/lib/solvents.lib Loading parameters: /opt/amber16/dat/leap/parm/frcmod.ionsjc_tip3p Reading force field modification type file (frcmod) Reading title: Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008) ----- 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 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 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: 13804 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 $*