Dear David,
> If you just name your ligand "LIG", reduce won't be able to help. If this
> really came from a pdb entry, us the residue name in the PDB entry: that
is
> what reduce knows about.
My ligand is new and it does not coe from a pdb entry.
I did docking to get protein-ligand complex.
> ??? Looks like you gave it a pdb file with more than just the ligand(?).
> I don't see any warnings like this when I run reduce on your "lig.pdb"
file.
What is your mean?
----------------------------------------------------------------------------------------------
I add H atoms using h_add in pymol (lig_h.pdb).
HETATM 1 N LIG A1100 25.838 24.320 115.794 1.00 0.00
N
HETATM 2 N LIG A1100 30.038 19.216 116.208 1.00 0.00
N
HETATM 3 N LIG A1100 30.295 17.907 115.854 1.00 0.00
N
HETATM 4 C LIG A1100 28.099 20.746 115.724 1.00 0.00
C
HETATM 5 C LIG A1100 26.984 20.842 116.556 1.00 0.00
C
HETATM 6 C LIG A1100 26.240 22.020 116.605 1.00 0.00
C
HETATM 7 C LIG A1100 26.580 23.117 115.812 1.00 0.00
C
HETATM 8 C LIG A1100 27.705 23.031 114.984 1.00 0.00
C
HETATM 9 C LIG A1100 28.459 21.851 114.942 1.00 0.00
C
HETATM 10 C LIG A1100 24.486 24.441 115.547 1.00 0.00
C
HETATM 11 C LIG A1100 23.883 25.803 115.499 1.00 0.00
C
HETATM 12 C LIG A1100 23.451 26.189 114.208 1.00 0.00
C
HETATM 13 C LIG A1100 22.787 27.392 113.983 1.00 0.00
C
HETATM 14 C LIG A1100 22.536 28.241 115.050 1.00 0.00
C
HETATM 15 C LIG A1100 22.952 27.883 116.333 1.00 0.00
C
HETATM 16 C LIG A1100 23.625 26.667 116.574 1.00 0.00
C
HETATM 17 C LIG A1100 24.040 26.405 117.972 1.00 0.00
C
HETATM 18 C LIG A1100 28.857 19.512 115.701 1.00 0.00
C
HETATM 19 C LIG A1100 29.276 17.519 115.116 1.00 0.00
C
HETATM 20 C LIG A1100 29.011 16.262 114.443 1.00 0.00
C
HETATM 21 C LIG A1100 27.883 16.110 113.623 1.00 0.00
C
HETATM 22 C LIG A1100 27.632 14.904 112.978 1.00 0.00
C
HETATM 23 C LIG A1100 28.501 13.829 113.148 1.00 0.00
C
HETATM 24 C LIG A1100 29.629 13.967 113.963 1.00 0.00
C
HETATM 25 C LIG A1100 29.887 15.180 114.602 1.00 0.00
C
HETATM 26 O LIG A1100 23.724 23.508 115.301 1.00 0.00
O
HETATM 27 O LIG A1100 24.654 25.435 118.372 1.00 0.00
O
HETATM 28 O LIG A1100 23.731 27.425 118.794 1.00 0.00
O
HETATM 29 O LIG A1100 28.313 18.482 114.991 1.00 0.00
O
HETATM 30 H LIG A1100 26.367 25.163 116.008 1.00 0.00
H
HETATM 31 H LIG A1100 23.257 28.075 118.235 1.00 0.00
H
HETATM 32 H01 LIG A1100 30.773 15.286 115.227 1.00 0.00
H
HETATM 33 H02 LIG A1100 26.692 19.991 117.172 1.00 0.00
H
HETATM 34 H03 LIG A1100 25.381 22.085 117.272 1.00 0.00
H
HETATM 35 H04 LIG A1100 27.995 23.884 114.370 1.00 0.00
H
HETATM 36 H05 LIG A1100 29.334 21.792 114.295 1.00 0.00
H
HETATM 37 H06 LIG A1100 23.644 25.525 113.365 1.00 0.00
H
HETATM 38 H07 LIG A1100 22.467 27.664 112.977 1.00 0.00
H
HETATM 39 H08 LIG A1100 22.016 29.185 114.887 1.00 0.00
H
HETATM 40 H09 LIG A1100 22.753 28.557 117.166 1.00 0.00
H
HETATM 41 H10 LIG A1100 27.196 16.946 113.490 1.00 0.00
H
HETATM 42 H11 LIG A1100 26.755 14.800 112.339 1.00 0.00
H
HETATM 43 H12 LIG A1100 28.302 12.882 112.647 1.00 0.00
H
HETATM 44 H13 LIG A1100 30.308 13.125 114.099 1.00 0.00
H
END
----------------------------------------------------------------------------------------------------
When I used following for only ligand:
$AMBERHOME/exe/antechamber -i lig_h.pdb -fi pdb -o lig_h.mol2 -fo mol2 -c
bcc -s 2
$AMBERHOME/exe/parmchk -i lig_h.mol2 -f mol2 -o lig_h.frcmod
$AMBERHOME/exe/tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.gaff
> source leaprc.gaff
> mods = loadAmberParams lig_h.frcmod
> lig = loadMol2 lig_h.mol2
> saveAmberParm lig lig_h.prmtop lig_h.inpcrd
> quit
lig_h.prmtop and lig_h.inpcrd files are created successfully and without
any errors and warnings.
----------------------------------------------------------------------------------------------------
Then, for the protein-ligand complex (comp.pdb), I used following:
$AMBERHOME/exe/antechamber -i lig_h.pdb -fi pdb -o lig_h.mol2 -fo mol2 -c
bcc -s 2
$AMBERHOME/exe/parmchk -i lig_h.mol2 -f mol2 -o lig_h.frcmod
$AMBERHOME/exe/tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff03.r1
> source leaprc.gaff
> mods = loadamberparams lig_h.frcmod
> lig = loadmol2 lig_h.mol2
> saveoff lig lig_h.lib
> saveamberparm lig lig_h.prmtop lig_h.inpcrd
> quit
$AMBERHOME/exe/tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff03.r1
> source leaprc.gaff
> mods = loadamberparams lig_h.frcmod
> loadoff lig_h.lib
> comp = loadpdb comp.pdb
Unknown residue: LIG number: 314 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Added missing heavy atom: .R<CASP 545>.A<OXT 13>
Creating new UNIT for residue: LIG sequence: 546
Created a new atom named: N within residue: .R<LIG 546>
Created a new atom named: C within residue: .R<LIG 546>
Created a new atom named: O within residue: .R<LIG 546>
Created a new atom named: H within residue: .R<LIG 546>
Created a new atom named: H01 within residue: .R<LIG 546>
Created a new atom named: H02 within residue: .R<LIG 546>
Created a new atom named: H03 within residue: .R<LIG 546>
Created a new atom named: H04 within residue: .R<LIG 546>
Created a new atom named: H05 within residue: .R<LIG 546>
Created a new atom named: H06 within residue: .R<LIG 546>
Created a new atom named: H07 within residue: .R<LIG 546>
Created a new atom named: H08 within residue: .R<LIG 546>
Created a new atom named: H09 within residue: .R<LIG 546>
Created a new atom named: H10 within residue: .R<LIG 546>
Created a new atom named: H11 within residue: .R<LIG 546>
Created a new atom named: H12 within residue: .R<LIG 546>
Created a new atom named: H13 within residue: .R<LIG 546>
total atoms in file: 5029
Leap added 13 missing atoms according to residue templates:
1 Heavy
12 H / lone pairs
The file contained 17 atoms not in residue templates
And then,
> saveamberparm comp comp.prmtop comp.inpcrd
Checking Unit.
WARNING: The unperturbed charge of the unit: -8.000003 is not zero.
FATAL: Atom .R<LIG 546>.A<N 1> does not have a type.
FATAL: Atom .R<LIG 546>.A<C 2> does not have a type.
FATAL: Atom .R<LIG 546>.A<O 3> does not have a type.
FATAL: Atom .R<LIG 546>.A<H 4> does not have a type.
FATAL: Atom .R<LIG 546>.A<H01 5> does not have a type.
FATAL: Atom .R<LIG 546>.A<H02 6> does not have a type.
FATAL: Atom .R<LIG 546>.A<H03 7> does not have a type.
FATAL: Atom .R<LIG 546>.A<H04 8> does not have a type.
FATAL: Atom .R<LIG 546>.A<H05 9> does not have a type.
FATAL: Atom .R<LIG 546>.A<H06 10> does not have a type.
FATAL: Atom .R<LIG 546>.A<H07 11> does not have a type.
FATAL: Atom .R<LIG 546>.A<H08 12> does not have a type.
FATAL: Atom .R<LIG 546>.A<H09 13> does not have a type.
FATAL: Atom .R<LIG 546>.A<H10 14> does not have a type.
FATAL: Atom .R<LIG 546>.A<H11 15> does not have a type.
FATAL: Atom .R<LIG 546>.A<H12 16> does not have a type.
FATAL: Atom .R<LIG 546>.A<H13 17> does not have a type.
Failed to generate parameters
Parameter file was not saved.
I don't have this problem for only ligand.
Best,
Atila
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Received on Thu Sep 17 2015 - 23:30:04 PDT
