Good day,
I would like to ask the users if there is anything wrong with the tleap run I performed (see below). If it is wrong please let me know how to fix it. I am a relatively new user.
Thank you.
Kind regards
Neal Broomhead
Welcome to LEaP!
Sourcing: ./tleap.all
----- Source: /apps/chpc/chem/amber/14/dat/leap/cmd/leaprc.ff99SB
----- Source of /apps/chpc/chem/amber/14/dat/leap/cmd/leaprc.ff99SB done
Log file: ./leap.log
Loading parameters: /apps/chpc/chem/amber/14/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99
Loading parameters: /apps/chpc/chem/amber/14/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
Loading library: /apps/chpc/chem/amber/14/dat/leap/lib/all_nucleic94.lib
Loading library: /apps/chpc/chem/amber/14/dat/leap/lib/all_amino94.lib
Loading library: /apps/chpc/chem/amber/14/dat/leap/lib/all_aminoct94.lib
Loading library: /apps/chpc/chem/amber/14/dat/leap/lib/all_aminont94.lib
Loading library: /apps/chpc/chem/amber/14/dat/leap/lib/ions94.lib
Loading library: /apps/chpc/chem/amber/14/dat/leap/lib/solvents.lib
----- Source: /apps/chpc/chem/amber/14/dat/leap/cmd/leaprc.gaff
----- Source of /apps/chpc/chem/amber/14/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /apps/chpc/chem/amber/14/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.7, Nov 2013)
Loading Mol2 file: ./LIG.mol2
Reading MOLECULE named complex.pdb
Could not open file LIG.frcmod: not found
Checking 'LIG'....
Checking parameters for unit 'LIG'.
Checking for bond parameters.
Checking for angle parameters.
Could not find angle parameter: c2 - cf - nh
There are missing parameters.
Unit is OK.
Loading PDB file: ./rec.pdb
Added missing heavy atom: .R<THR 407>.A<CG2 7>
Added missing heavy atom: .R<THR 407>.A<OG1 11>
Added missing heavy atom: .R<CTYR 574>.A<OXT 22>
total atoms in file: 3243
Leap added 3246 missing atoms according to residue templates:
3 Heavy
3243 H / lone pairs
Using H(N)-modified Bondi radii
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Could not find angle parameter: c2 - cf - nh
Building proper torsion parameters.
** No torsion terms for c2-cf-cd-cc
** No torsion terms for c2-cf-cd-nd
** No torsion terms for c2-cf-nh-c3
** No torsion terms for c2-cf-nh-hn
** No torsion terms for cc-cd-cf-nh
** No torsion terms for cd-cf-nh-c3
** No torsion terms for cd-cf-nh-hn
** No torsion terms for nh-cf-cd-nd
** No torsion terms for nd-cc-oh-ho
** No torsion terms for na-cc-oh-ho
Building improper torsion parameters.
total 10 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Parameter file was not saved.
Loading PDB file: ./rec.pdb
Added missing heavy atom: .R<THR 407>.A<CG2 7>
Added missing heavy atom: .R<THR 407>.A<OG1 11>
Added missing heavy atom: .R<CTYR 574>.A<OXT 22>
total atoms in file: 3243
Leap added 3246 missing atoms according to residue templates:
3 Heavy
3243 H / lone pairs
Checking Unit.
WARNING: There is a bond of 9.697454 angstroms between:
------- .R<GLY 406>.A<C 6> and .R<THR 407>.A<N 1>
WARNING: There is a bond of 5.446103 angstroms between:
------- .R<ARG 530>.A<C 23> and .R<ASN 531>.A<N 1>
WARNING: The unperturbed charge of the unit: -7.000000 is not zero.
-- ignoring the warnings.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 1289 improper torsions applied
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
CTYR 1
NMET 1
)
(no restraints)
Checking Unit.
WARNING: There is a bond of 5.446103 angstroms between:
------- .R<ARG 530>.A<C 23> and .R<ASN 531>.A<N 1>
WARNING: There is a bond of 9.697454 angstroms between:
------- .R<GLY 406>.A<C 6> and .R<THR 407>.A<N 1>
WARNING: The unperturbed charge of the unit: -7.002999 is not zero.
-- ignoring the warnings.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Could not find angle parameter: c2 - cf - nh
Building proper torsion parameters.
** No torsion terms for na-cc-oh-ho
** No torsion terms for nd-cc-oh-ho
** No torsion terms for nh-cf-cd-nd
** No torsion terms for cd-cf-nh-c3
** No torsion terms for cd-cf-nh-hn
** No torsion terms for cc-cd-cf-nh
** No torsion terms for c2-cf-cd-cc
** No torsion terms for c2-cf-cd-nd
** No torsion terms for c2-cf-nh-c3
** No torsion terms for c2-cf-nh-hn
Building improper torsion parameters.
total 1299 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Parameter file was not saved.
Writing pdb file: complex_gas.pdb
Converting N-terminal residue name to PDB format: NMET -> MET
Converting C-terminal residue name to PDB format: CTYR -> TYR
Total unperturbed charge: -7.002999
Total perturbed charge: -7.002999
7 Na+ ions required to neutralize.
Adding 7 counter ions to "complex" using 1A grid
Grid extends from solute vdw + 1.87 to 7.87
Resolution: 1.00 Angstrom.
grid build: 1 sec
Calculating grid charges
charges: 11 sec
Placed Na+ in complex at (1.75, -28.52, 12.49).
Placed Na+ in complex at (-13.25, -32.52, 5.49).
Placed Na+ in complex at (32.75, -19.52, 42.49).
Placed Na+ in complex at (2.75, -32.52, 19.49).
Placed Na+ in complex at (-12.25, -31.52, 31.49).
Placed Na+ in complex at (40.75, -13.52, 13.49).
Placed Na+ in complex at (-8.25, 4.48, 15.49).
Done adding ions.
Solute vdw bounding box: 82.246 69.393 48.661
Total bounding box for atom centers: 98.246 85.393 64.661
Solvent unit box: 18.774 18.774 18.774
Total vdw box size: 100.998 88.481 67.771 angstroms.
Volume: 605634.016 A^3
Total mass 299155.838 amu, Density 0.820 g/cc
Added 14006 residues.
Checking Unit.
WARNING: There is a bond of 5.446103 angstroms between:
------- .R<ARG 530>.A<C 23> and .R<ASN 531>.A<N 1>
WARNING: There is a bond of 9.697454 angstroms between:
------- .R<GLY 406>.A<C 6> and .R<THR 407>.A<N 1>
-- ignoring the warnings.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Could not find angle parameter: c2 - cf - nh
Building proper torsion parameters.
** No torsion terms for na-cc-oh-ho
** No torsion terms for nd-cc-oh-ho
** No torsion terms for nh-cf-cd-nd
** No torsion terms for cd-cf-nh-c3
** No torsion terms for cd-cf-nh-hn
** No torsion terms for cc-cd-cf-nh
** No torsion terms for c2-cf-cd-cc
** No torsion terms for c2-cf-cd-nd
** No torsion terms for c2-cf-nh-c3
** No torsion terms for c2-cf-nh-hn
Building improper torsion parameters.
total 1299 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Parameter file was not saved.
Writing pdb file: com_solvated.pdb
Converting N-terminal residue name to PDB format: NMET -> MET
Converting C-terminal residue name to PDB format: CTYR -> TYR
Quit
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Received on Thu Apr 14 2016 - 03:00:03 PDT
