Hi
While generating ligand parameters, I am facing some angle parameters
errors, I used the following commands
*antechamber -i 2888695.pdb -fi pdb -o 2888695.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
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: 156; 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
* parmchk -i 2888695.mol2 -f mol2 -o 2888695.frcmod*
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 2888695.mol2*
Loading Mol2 file: ./2888695.mol2
Reading MOLECULE named LIG
antechamber -i 2888695.pdb -fi pdb -o 2888695.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
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: 156; 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
parmchk -i 2888695.mol2 -f mol2 -o 2888695.frcmod
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 2888695.mol2*
Loading Mol2 file: ./2888695.mol2
Reading MOLECULE named LIG
> check LIG
Checking 'LIG'....
Warning: Close contact of 1.351881 angstroms between .R<LIG 1>.A<N1 2> and
.R<LIG 1>.A<C6 10>
Warning: Close contact of 1.411730 angstroms between .R<LIG 1>.A<C2 4> and
.R<LIG 1>.A<C3 6>
Warning: Close contact of 1.486072 angstroms between .R<LIG 1>.A<C3 6> and
.R<LIG 1>.A<C5 9>
Warning: Close contact of 1.450377 angstroms between .R<LIG 1>.A<C10 14>
and .R<LIG 1>.A<C12 16>
Warning: Close contact of 1.316128 angstroms between .R<LIG 1>.A<C13 17>
and .R<LIG 1>.A<C14 18>
Checking parameters for unit 'LIG'.
Checking for bond parameters.
Checking for angle parameters.
Could not find angle parameter: s - c2 - c1
Could not find angle parameter: n3 - c2 - c1
Could not find angle parameter: c3 - c1 - ha
Could not find angle parameter: c3 - c1 - ha
Could not find angle parameter: ha - c1 - ha
Could not find angle parameter: ha - c1 - ha
There are missing parameters.
check: Warnings: 5
Unit is OK.
*> loadamberparams 2888695.frcmod*
Loading parameters: ./2888695.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
*> saveoff LIG 2888695.lib*
Creating 2888695.lib
Building topology.
Building atom parameters.
*> saveamberparm LIG 2888695.prmtop 2888695.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
gedit 2888695_complex.pdb 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 2888695.frcmod*
Loading parameters: ./2888695.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
*> loadoff 2888695.lib*
Loading library: ./2888695.lib
*> complex = loadpdb 2888695_complex.pdb *
Loading PDB file: ./2888695_complex.pdb
(starting new molecule for chain A)
Added missing heavy atom: .R<CPRO 552>.A<CD 2>
Added missing heavy atom: .R<CPRO 552>.A<CA 11>
Added missing heavy atom: .R<CPRO 552>.A<CG 5>
Added missing heavy atom: .R<CPRO 552>.A<CB 8>
Added missing heavy atom: .R<CPRO 552>.A<C 13>
Added missing heavy atom: .R<CPRO 552>.A<O 14>
Added missing heavy atom: .R<CPRO 552>.A<OXT 15>
total atoms in file: 2022
Leap added 2036 missing atoms according to residue templates:
7 Heavy
2029 H / lone pairs
*> saveamberparm complex 2888695_complex.prmtop 2888695_complex.inpcrd*
Checking Unit.
WARNING: The unperturbed charge of the unit: -5.999000 is not zero.
-- ignoring the warning.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Could not find angle parameter: c1 - s - c2
Could not find angle parameter: c2 - c1 - ha
Could not find angle parameter: c2 - c1 - ha
Could not find angle parameter: n1 - c1 - s
Building proper torsion parameters.
** No torsion terms for c1-s-c2-c2
** No torsion terms for c1-s-c2-c1
** No torsion terms for c1-c1-s-c2
** No torsion terms for c2-c1-n1-c1
** No torsion terms for c1-n1-c1-c1
** No torsion terms for c1-c1-n1-c1
** No torsion terms for s-c1-n1-c1
** No torsion terms for n1-c1-s-c2
Building improper torsion parameters.
total 748 improper torsions applied
Building H-Bond parameters.
Parameter file was not saved.
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Received on Sun Nov 18 2018 - 19:30:03 PST
