umer@umer01:~> cd Desktop/local_machine/1GEQ_LB_ 1GEQ_LB_137/ 1GEQ_LB_F19/ 1GEQ_LB_F9F/ 1GEQ_LB_HPF/ 1GEQ_LB_IGP/ umer@umer01:~> cd Desktop/local_machine/1GEQ_LB_F9F/ umer@umer01:~/Desktop/local_machine/1GEQ_LB_F9F> ls 1GEQ_F9F.crd 1GEQ_F9F.pdb 1GEQ_F9F.prmtop 1GEQ_f9f_wat.pdb all_min.out complex.crd complex.prmtop F9F_H.prepin leap.log 1GEQ_F9F.inpcrd ~1GEQ_F9F.prmtop 1GEQ_F9F_water.pdb all_min.namd command complex.inpcrd F9F_H.frcmod inpcrd umer@umer01:~/Desktop/local_machine/1GEQ_LB_F9F> tleap -I: Adding /usr/local/amber12/dat/leap/prep to search path. -I: Adding /usr/local/amber12/dat/leap/lib to search path. -I: Adding /usr/local/amber12/dat/leap/parm to search path. -I: Adding /usr/local/amber12/dat/leap/cmd to search path. Welcome to LEaP! (no leaprc in search path) > source leaprc.gaff ----- Source: /usr/local/amber12/dat/leap/cmd/leaprc.gaff ----- Source of /usr/local/amber12/dat/leap/cmd/leaprc.gaff done Log file: ./leap.log Loading parameters: /usr/local/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 F9F_H.frcmod Loading parameters: ./F9F_H.frcmod Reading force field modification type file (frcmod) Reading title: remark goes here > source leaprc.ff10 ----- Source: /usr/local/amber12/dat/leap/cmd/leaprc.ff10 ----- Source of /usr/local/amber12/dat/leap/cmd/leaprc.ff10 done Log file: ./leap.log Loading parameters: /usr/local/amber12/dat/leap/parm/parm10.dat Reading title: PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA Loading library: /usr/local/amber12/dat/leap/lib/amino10.lib Loading library: /usr/local/amber12/dat/leap/lib/aminoct10.lib Loading library: /usr/local/amber12/dat/leap/lib/aminont10.lib Loading library: /usr/local/amber12/dat/leap/lib/phosphoaa10.lib Loading library: /usr/local/amber12/dat/leap/lib/nucleic10.lib Loading library: /usr/local/amber12/dat/leap/lib/ions08.lib Loading library: /usr/local/amber12/dat/leap/lib/solvents.lib > loadamberparams F9F_H.frcmod Loading parameters: ./F9F_H.frcmod Reading force field modification type file (frcmod) Reading title: remark goes here > pro = loadpdb 1GEQ_F9F.pdb Loading PDB file: ./1GEQ_F9F.pdb Unknown residue: F9F number: 248 type: Terminal/last ..relaxing end constraints to try for a dbase match -no luck Added missing heavy atom: .R.A Creating new UNIT for residue: F9F sequence: 249 Created a new atom named: C1 within residue: .R Created a new atom named: C2 within residue: .R Created a new atom named: C3 within residue: .R Created a new atom named: C4 within residue: .R Created a new atom named: C5 within residue: .R Created a new atom named: C6 within residue: .R Created a new atom named: S12 within residue: .R Created a new atom named: O21 within residue: .R Created a new atom named: O22 within residue: .R Created a new atom named: N13 within residue: .R Created a new atom named: C14 within residue: .R Created a new atom named: C15 within residue: .R Created a new atom named: O16 within residue: .R Created a new atom named: P17 within residue: .R Created a new atom named: O20 within residue: .R Created a new atom named: O19 within residue: .R Created a new atom named: O18 within residue: .R Created a new atom named: O7 within residue: .R Created a new atom named: C8 within residue: .R Created a new atom named: F10 within residue: .R Created a new atom named: F9F within residue: .R Created a new atom named: F11 within residue: .R total atoms in file: 1963 Leap added 1999 missing atoms according to residue templates: 1 Heavy 1998 H / lone pairs The file contained 22 atoms not in residue templates > loadamberparams F9F_H.frcmod Loading parameters: ./F9F_H.frcmod Reading force field modification type file (frcmod) Reading title: remark goes here > charge pro Total unperturbed charge: 3.000000 Total perturbed charge: 3.000000 > addions pro Cl- 3 Using default radius 1.50 for ion Cl- Adding 3 counter ions to "pro" using 1A grid Used default radius 1.50 for 22 atoms Grid extends from solute vdw + 1.50 to 7.50 Resolution: 1.00 Angstrom. grid build: 1 sec (no solvent present) Calculating grid charges charges: 4 sec Placed Cl- in pro at (42.84, 28.47, 60.11). Placed Cl- in pro at (55.84, 30.47, 80.11). Placed Cl- in pro at (69.84, 29.47, 44.11). Done adding ions. > solvatebox pro TIP3PBOX 12 (using default radius 1.500000 for C1) (using default radius 1.500000 for C2) (using default radius 1.500000 for C3) (using default radius 1.500000 for C4) (using default radius 1.500000 for C5) (using default radius 1.500000 for C6) (using default radius 1.500000 for S12) (using default radius 1.500000 for O21) (using default radius 1.500000 for O22) (using default radius 1.500000 for N13) (using default radius 1.500000 for C14) (using default radius 1.500000 for C15) (using default radius 1.500000 for O16) (using default radius 1.500000 for P17) (using default radius 1.500000 for O20) (using default radius 1.500000 for O19) (using default radius 1.500000 for O18) (using default radius 1.500000 for O7) (using default radius 1.500000 for C8) (using default radius 1.500000 for F10) (using default radius 1.500000 for F9F) (using default radius 1.500000 for F11) (using default radius 1.500000 for Cl-) (using default radius 1.500000 for Cl-) (using default radius 1.500000 for Cl-) Solute vdw bounding box: 52.279 49.411 54.925 Total bounding box for atom centers: 76.279 73.411 78.925 Solvent unit box: 18.774 18.774 18.774 (using default radius 1.500000 for C1) (using default radius 1.500000 for C2) (using default radius 1.500000 for C3) (using default radius 1.500000 for C4) (using default radius 1.500000 for C5) (using default radius 1.500000 for C6) (using default radius 1.500000 for S12) (using default radius 1.500000 for O21) (using default radius 1.500000 for O22) (using default radius 1.500000 for N13) (using default radius 1.500000 for C14) (using default radius 1.500000 for C15) (using default radius 1.500000 for O16) (using default radius 1.500000 for P17) (using default radius 1.500000 for O20) (using default radius 1.500000 for O19) (using default radius 1.500000 for O18) (using default radius 1.500000 for O7) (using default radius 1.500000 for C8) (using default radius 1.500000 for F10) (using default radius 1.500000 for F9F) (using default radius 1.500000 for F11) (using default radius 1.500000 for Cl-) (using default radius 1.500000 for Cl-) (using default radius 1.500000 for Cl-) Total vdw box size: 79.094 76.664 81.867 angstroms. Volume: 496417.355 A^3 Mass > 245980.076 amu, Density > 0.823 g/cc (type - hence mass - of one or more atoms could not be found) Added 12127 residues. > savepdb protein.pdb savePdb: Improper number of arguments! usage: savePdb > savepdb pro protein.pdb Writing pdb file: protein.pdb Converting N-terminal residue name to PDB format: NMET -> MET Converting C-terminal residue name to PDB format: CILE -> ILE > saveamberparm pro protein.prmtop protein.inpcrd Checking Unit. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. FATAL: Atom .R.A does not have a type. Failed to generate parameters Parameter file was not saved. >