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tleap.LOG
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tleap.LOG
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-I: Adding /miniconda3/dat/leap/prep to search path.
-I: Adding /miniconda3/dat/leap/lib to search path.
-I: Adding /miniconda3/dat/leap/parm to search path.
-I: Adding /miniconda3/dat/leap/cmd to search path.
-f: Source tleap_script.txt.
Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./tleap_script.txt
----- Source: /miniconda3/dat/leap/cmd/leaprc.protein.ff14sb
----- Source of /miniconda3/dat/leap/cmd/leaprc.protein.ff14sb done
Log file: ./leap.log
Loading parameters: /miniconda3/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading parameters: /miniconda3/dat/leap/parm/frcmod.ff14SB
Reading force field modification type file (frcmod)
Reading title:
ff14SB protein backbone and sidechain parameters
Loading library: /miniconda3/dat/leap/lib/amino12.lib
Loading library: /miniconda3/dat/leap/lib/aminoct12.lib
Loading library: /miniconda3/dat/leap/lib/aminont12.lib
----- Source: /miniconda3/dat/leap/cmd/leaprc.water.tip3p
----- Source of /miniconda3/dat/leap/cmd/leaprc.water.tip3p done
Loading library: /miniconda3/dat/leap/lib/atomic_ions.lib
Loading library: /miniconda3/dat/leap/lib/solvents.lib
Loading parameters: /miniconda3/dat/leap/parm/frcmod.tip3p
Reading force field modification type file (frcmod)
Reading title:
This is the additional/replacement parameter set for TIP3P water
Loading parameters: /miniconda3/dat/leap/parm/frcmod.ions1lm_126_tip3p
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of monovalent ions for TIP3P water model (12-6 normal usage set)
Loading parameters: /miniconda3/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)
Loading parameters: /miniconda3/dat/leap/parm/frcmod.ions234lm_126_tip3p
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water model (12-6 normal usage set)
Loading Prep file: ./tleap_prep/rf.prepin
Loading Prep file: ./tleap_prep/sf.prepin
Loading parameters: ./tleap_prep/F.frcmod
Reading force field modification type file (frcmod)
Reading title:
Force field parameters from rf2.prmtop
Solute vdw bounding box: 10.288 8.934 7.544
Total bounding box for atom centers: 30.288 28.934 27.544
Solvent unit box: 18.774 18.774 18.774
Total vdw box size: 32.955 32.158 30.276 angstroms.
Volume: 32085.586 A^3
Total mass 12511.148 amu, Density 0.648 g/cc
Added 684 residues.
Writing pdb file: amber_ff/amber.pdb
printing CRYST1 record to PDB file with box info
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
old PREP-specified impropers:
<PRF 2>: -M CA N CD
<PRF 2>: CA +M C O
total 4 improper torsions applied
2 improper torsions in old prep form
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
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
WAT 684
)
(no restraints)
Quit
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.