antechamber -i ../ligand2.pdb -fi pdb -o ligand.mol2 -fo mol2 -c bcc -s 2 Running: /opt/apps/amber/amber12//bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac For atom[23]:O, the best APS is not zero, bonds involved by this atom are frozen Warning: the assigned bond types may be wrong, please : (1) double check the structure (the connectivity) and/or (2) adjust atom valence penalty parameters in APS.DAT, and/or (3) increase PSCUTOFF in define.h and recompile bondtype.c Be cautious, use a large value of PSCUTOFF (>100) will significantly increase the computation time Running: /opt/apps/amber/amber12//bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff Total number of electrons: 184; net charge: 0 Running: /opt/apps/amber/amber12//bin/sqm -O -i sqm.in -o sqm.out Running: /opt/apps/amber/amber12//bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /opt/apps/amber/amber12//dat/antechamber/BCCPARM.DAT -s 2 -j 1 Running: /opt/apps/amber/amber12//bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC [shivangi@ilshpcc trying_ZN]$ parmchk -i ligand.mol2 -f mol2 -o ligand.frcmod [shivangi@ilshpcc trying_ZN]$ tleap -I: Adding /opt/apps/amber/amber12//dat/leap/prep to search path. -I: Adding /opt/apps/amber/amber12//dat/leap/lib to search path. -I: Adding /opt/apps/amber/amber12//dat/leap/parm to search path. -I: Adding /opt/apps/amber/amber12//dat/leap/cmd to search path. Welcome to LEaP! (no leaprc in search path) > source leaprc.ff99SB ----- Source: /opt/apps/amber/amber12//dat/leap/cmd/leaprc.ff99SB ----- Source of /opt/apps/amber/amber12//dat/leap/cmd/leaprc.ff99SB done Log file: ./leap.log Loading parameters: /opt/apps/amber/amber12//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/apps/amber/amber12//dat/leap/parm/frcmod.ff99SB Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) Loading library: /opt/apps/amber/amber12//dat/leap/lib/all_nucleic94.lib Loading library: /opt/apps/amber/amber12//dat/leap/lib/all_amino94.lib Loading library: /opt/apps/amber/amber12//dat/leap/lib/all_aminoct94.lib Loading library: /opt/apps/amber/amber12//dat/leap/lib/all_aminont94.lib Loading library: /opt/apps/amber/amber12//dat/leap/lib/ions94.lib Loading library: /opt/apps/amber/amber12//dat/leap/lib/solvents.lib > source leaprc.gaff ----- Source: /opt/apps/amber/amber12//dat/leap/cmd/leaprc.gaff ----- Source of /opt/apps/amber/amber12//dat/leap/cmd/leaprc.gaff done Log file: ./leap.log Loading parameters: /opt/apps/amber/amber12//dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic molecules (Version 1.4, March 2010) add. info. at the end > LIG=loadmol2 ligand.mol2 Loading Mol2 file: ./ligand.mol2 Reading MOLECULE named LIG > check LIG Checking 'LIG'.... Warning: Close contact of 1.421451 angstroms between .R.A and .R.A Warning: Close contact of 1.360874 angstroms between .R.A and .R.A Warning: Close contact of 1.401729 angstroms between .R.A and .R.A Warning: Close contact of 1.459893 angstroms between .R.A and .R.A Warning: Close contact of 1.228761 angstroms between .R.A and .R.A Warning: Close contact of 1.407621 angstroms between .R.A and .R.A Warning: Close contact of 1.407999 angstroms between .R.A and .R.A Warning: Close contact of 1.407067 angstroms between .R.A and .R.A Warning: Close contact of 1.408847 angstroms between .R.A and .R.A Warning: Close contact of 1.411834 angstroms between .R.A and .R.A Warning: Close contact of 1.408876 angstroms between .R.A and .R.A Warning: Close contact of 1.406494 angstroms between .R.A and .R.A Warning: Close contact of 1.407992 angstroms between .R.A and .R.A Warning: Close contact of 1.408345 angstroms between .R.A and .R.A Checking parameters for unit 'LIG'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 14 Unit is OK. > loadamberparams ligand.frcmod Loading parameters: ./ligand.frcmod Reading force field modification type file (frcmod) Reading title: remark goes here > saveoff LIG ligand.lib Creating ligand.lib Building topology. Building atom parameters. > saveamberparm LIG ligand.prmtop ligand.inpcrd Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 3 improper torsions applied Building H-Bond parameters. Not Marking per-residue atom chain types. Marking per-residue atom chain types. (Residues lacking connect0/connect1 - these don't have chain types marked: res total affected LIG 1 ) (no restraints) > quit Quit [shivangi@ilshpcc trying_ZN]$ tleap -I: Adding /opt/apps/amber/amber12//dat/leap/prep to search path. -I: Adding /opt/apps/amber/amber12//dat/leap/lib to search path. -I: Adding /opt/apps/amber/amber12//dat/leap/parm to search path. -I: Adding /opt/apps/amber/amber12//dat/leap/cmd to search path. Welcome to LEaP! (no leaprc in search path) > i = createAtom ZN Zn2+ 2.0 > set i element "Zn" > set i position { 0 0 0 } > r = createResidue ZN > add r i > ZN = createUnit ZN > add ZN r > saveOff ZN ./atomic_ions.lib Creating ./atomic_ions.lib Building topology. Building atom parameters. > quit [shivangi@ilshpcc trying_ZN]$ tleap -I: Adding /opt/apps/amber/amber12//dat/leap/prep to search path. -I: Adding /opt/apps/amber/amber12//dat/leap/lib to search path. -I: Adding /opt/apps/amber/amber12//dat/leap/parm to search path. -I: Adding /opt/apps/amber/amber12//dat/leap/cmd to search path. Welcome to LEaP! (no leaprc in search path) > source leaprc.ff99SB ----- Source: /opt/apps/amber/amber12//dat/leap/cmd/leaprc.ff99SB ----- Source of /opt/apps/amber/amber12//dat/leap/cmd/leaprc.ff99SB done Log file: ./leap.log Loading parameters: /opt/apps/amber/amber12//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/apps/amber/amber12//dat/leap/parm/frcmod.ff99SB Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) Loading library: /opt/apps/amber/amber12//dat/leap/lib/all_nucleic94.lib Loading library: /opt/apps/amber/amber12//dat/leap/lib/all_amino94.lib Loading library: /opt/apps/amber/amber12//dat/leap/lib/all_aminoct94.lib Loading library: /opt/apps/amber/amber12//dat/leap/lib/all_aminont94.lib Loading library: /opt/apps/amber/amber12//dat/leap/lib/ions94.lib Loading library: /opt/apps/amber/amber12//dat/leap/lib/solvents.lib > source leaprc.gaff ----- Source: /opt/apps/amber/amber12//dat/leap/cmd/leaprc.gaff ----- Source of /opt/apps/amber/amber12//dat/leap/cmd/leaprc.gaff done Log file: ./leap.log Loading parameters: /opt/apps/amber/amber12//dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic molecules (Version 1.4, March 2010) add. info. at the end > loadamberparams ligand.frcmod Loading parameters: ./ligand.frcmod Reading force field modification type file (frcmod) Reading title: remark goes here > loadoff ligand.lib Loading library: ./ligand.lib > loadoff atomic_ions.lib Loading library: ./atomic_ions.lib > complex =loadpdb 18_final_complex_2_noH.pdb Loading PDB file: ./18_final_complex_2_noH.pdb (starting new molecule for chain ) -- residue 274: duplicate [ C] atoms (total 17) -- residue 274: duplicate [ N] atoms (total 5) -- residue 274: duplicate [ O] atoms (total 4) Warning: Atom names in each residue should be unique. (Same-name atoms are handled by using the first occurrence and by ignoring the rest. Frequently duplicate atom names stem from alternate conformations in the PDB file.) Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A Added missing heavy atom: .R.A total atoms in file: 1981 Leap added 1975 missing atoms according to residue templates: 30 Heavy 1945 H / lone pairs > saveamberparm complex rec_lig.prmtop rec_lig.inpcrd Checking Unit. WARNING: There is a bond of 5.921247 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 3.779667 angstroms between: ------- .R.A and .R.A WARNING: There is a bond of 9.657179 angstroms between: ------- .R.A and .R.A WARNING: The unperturbed charge of the unit: -5.998999 is not zero. -- ignoring the warnings. Building topology. Building atom parameters. For atom: .R.A Could not find type: Zn2+ Parameter file was not saved.