~/Documents/latex/doc/papers/2009/yank/test-systems/T4-lysozyme-L99A/amber-explicit ~/Documents/latex/doc/papers/2009/yank/test-systems/T4-lysozyme-L99A/amber-explicit -I: Adding /Users/jchodera/local/src/amber10/dat/leap/prep to search path. -I: Adding /Users/jchodera/local/src/amber10/dat/leap/lib to search path. -I: Adding /Users/jchodera/local/src/amber10/dat/leap/parm to search path. -I: Adding /Users/jchodera/local/src/amber10/dat/leap/cmd to search path. -f: Source setup.leap.in. Welcome to LEaP! (no leaprc in search path) Sourcing: ./setup.leap.in ----- Source: /Users/jchodera/local/src/amber10/dat/leap/cmd/leaprc.ff96 ----- Source of /Users/jchodera/local/src/amber10/dat/leap/cmd/leaprc.ff96 done Log file: ./leap.log Loading parameters: /Users/jchodera/local/src/amber10/dat/leap/parm/parm96.dat Reading title: PARM96 for DNA, RNA and proteins with TIP3P Water. USE SCEE=1.2 in energy progs Loading library: /Users/jchodera/local/src/amber10/dat/leap/lib/all_nucleic94.lib Loading library: /Users/jchodera/local/src/amber10/dat/leap/lib/all_amino94.lib Loading library: /Users/jchodera/local/src/amber10/dat/leap/lib/all_aminoct94.lib Loading library: /Users/jchodera/local/src/amber10/dat/leap/lib/all_aminont94.lib Loading library: /Users/jchodera/local/src/amber10/dat/leap/lib/ions94.lib Loading library: /Users/jchodera/local/src/amber10/dat/leap/lib/solvents.lib ----- Source: /Users/jchodera/local/src/amber10/dat/leap/cmd/leaprc.gaff ----- Source of /Users/jchodera/local/src/amber10/dat/leap/cmd/leaprc.gaff done Log file: ./leap.log Loading parameters: /Users/jchodera/local/src/amber10/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic mol., add. info. at the end (June, 2003) Loading PDB file: ./receptor.pdb total atoms in file: 1290 Leap added 1313 missing atoms according to residue templates: 1313 H / lone pairs Loading parameters: ./ligand.frcmod Reading force field modification type file (frcmod) Reading title: remark goes here Loading parameters: ./ligand.frcmod Reading force field modification type file (frcmod) Reading title: remark goes here Loading Mol2 file: ./ligand.mol2 Reading MOLECULE named TMP Checking 'complex'.... WARNING: The unperturbed charge of the unit: 8.000000 is not zero. Warning: Close contact of 1.518782 angstroms between .R.A and .R.A Warning: Close contact of 2.072268 angstroms between .R.A and .R.A Checking parameters for unit 'complex'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 3 Unit is OK. Total unperturbed charge: 8.000000 Total perturbed charge: 8.000000 Solute vdw bounding box: 40.288 44.319 54.458 Total bounding box for atom centers: 56.288 60.319 70.458 Solvent unit box: 18.774 18.774 18.774 Total vdw box size: 58.950 63.133 73.748 angstroms. Volume: 274468.580 A^3 Total mass 131608.910 amu, Density 0.796 g/cc Added 6282 residues. 8 Cl- ions required to neutralize. Adding 8 counter ions to "complex" using 1A grid Grid extends from solute vdw + 5.14 to 11.14 Resolution: 1.00 Angstrom. grid build: 0 sec Solvent present: replacing closest with ion when steric overlaps occur Calculating grid charges charges: 7 sec (Replacing solvent molecule) Placed Cl- in complex at (21.73, 6.75, 4.92). (Replacing solvent molecule) Placed Cl- in complex at (-21.15, -3.59, -16.10). (Replacing solvent molecule) Placed Cl- in complex at (18.56, 17.33, 10.84). (Replacing solvent molecule) Placed Cl- in complex at (9.93, -25.06, -5.21). (Replacing solvent molecule) Placed Cl- in complex at (-14.93, -22.46, -16.45). (Replacing solvent molecule) Placed Cl- in complex at (16.40, -3.59, -16.10). (Replacing solvent molecule) Placed Cl- in complex at (-9.84, -1.29, -23.99). (Replacing solvent molecule) Placed Cl- in complex at (14.70, 18.18, 2.76). Done adding ions. Checking 'complex'.... Warning: Close contact of 1.518782 angstroms between .R.A and .R.A Warning: Close contact of 2.072268 angstroms between .R.A and .R.A Checking parameters for unit 'complex'. Checking for bond parameters. Checking for angle parameters. check: Warnings: 2 Unit is OK. Total unperturbed charge: -0.000000 Total perturbed charge: -0.000000 Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 6 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 TMP 1 ) (no restraints) Checking Unit. WARNING: The unperturbed charge of the unit: 8.000000 is not zero. -- ignoring the warning. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 516 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 CLYS 1 NMET 1 ) (no restraints) Checking Unit. Building topology. Building atom parameters. Building bond parameters. Building angle parameters. Building proper torsion parameters. Building improper torsion parameters. total 522 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 CLYS 1 NMET 1 TMP 1 WAT 6274 ) (no restraints) Quit ~/Documents/latex/doc/papers/2009/yank/test-systems/T4-lysozyme-L99A/amber-explicit