Dear all,
I am trying to prepare the input files for amber simulation on a protein-ligand. The ligand is named G39 in the pdb file. I used R.E.D. server to generate the mol2 file (Mol_m1-o1.mol2) and then used parmchk to produce the frcmod file. Next I tried to use tleap, and the leap.in file is:
source leaprc.gaffsource leaprc.ff10loadamberparams frcmodMOL = loadmol2 Mol_m1-o1.mol2comp = loadpdb complex.pdbbond comp.92.SG comp.417.SGbond comp.124.SG comp.129.SGbond comp.183.SG comp.230.SGbond comp.232.SG comp.237.SGbond comp.91.SG comp.417.SGbond comp.124.SG comp.129.SGbond comp.183.SG comp.230.SGbond comp.232.SG comp.237.SGbond comp.278.SG comp.291.SGbond comp.91.SG comp.417.SGbond comp.280.SG comp.289.SGbond comp.318.SG comp.336.SGbond comp.421.SG comp.447.SGsolvatebox comp TIP3PBOX 10.0addions comp Na+ 0saveoff comp 3cl0.offsaveamberparm comp 3cl0.prmtop 3cl0.inpcrdquit
However, when I run tleap -s -f leap.in, I get the follow output:
Loading parameters: ./frcmodReading force field modification type file (frcmod)Reading title:remark goes hereLoading Mol2 file: ./Mol_m1-o1.mol2Reading MOLECULE named G39Loading PDB file: ./3cl0_H274Y_N1_H_SG_noh.pdbUnknown residue: CA number: 385 type: NonterminalUnknown residue: G39 number: 386 type: NonterminalCreated a new atom named: OXT within residue: .R<ILE 467>Creating new UNIT for residue: CA sequence: 468One sided connection. Residue: missing connect0 atom.Created a new atom named: CA within residue: .R<CA 468>Creating new UNIT for residue: G39 sequence: 469Created a new atom named: C1 within residue: .R<G39 469>Created a new atom named: O1A within residue: .R<G39 469>Created a new atom named: O1B within residue: .R<G39 469>Created a new atom named: C2 within residue: .R<G39 469>Created a new atom named: C3 within residue: .R<G39 469>Created a new atom named: C4 within residue: .R<G39 469>Created a new atom named: C5 within residue: .R<G39 469>Created a new atom named: N5 within residue: .R<G39 469>Created a new atom named: C10 within residue: .R<G39 469>Created a new atom named: O10 within residue: .R<G39 469>Created a new atom named: C11 within residue: .R<G39 469>Created a new atom named: C6 within residue: .R<G39 469>Created a new atom named: C7 within residue: .R<G39 469>Created a new atom named: O7 within residue: .R<G39 469>Created a new atom named: C8 within residue: .R<G39 469>Created a new atom named: C9 within residue: .R<G39 469>Created a new atom named: C81 within residue: .R<G39 469>Created a new atom named: C82 within residue: .R<G39 469>Created a new atom named: C91 within residue: .R<G39 469>Created a new atom named: N4 within residue: .R<G39 469> total atoms in file: 3161 Leap added 3138 missing atoms according to residue templates: 3138 H / lone pairs The file contained 22 atoms not in residue templatesbond: Argument #1 is type String must be of type: [atom]usage: bond <atom1> <atom2> [order]bond: Argument #1 is type String must be of type: [atom]usage: bond <atom1> <atom2> [order]bond: Argument #1 is type String must be of type: [atom]usage: bond <atom1> <atom2> [order]bond: Argument #1 is type String must be of type: [atom]usage: bond <atom1> <atom2> [order]bond: Argument #1 is type String must be of type: [atom]usage: bond <atom1> <atom2> [order]bond: Argument #1 is type String must be of type: [atom]usage: bond <atom1> <atom2> [order]bond: Argument #1 is type String must be of type: [atom]usage: bond <atom1> <atom2> [order]bond: Argument #1 is type String must be of type: [atom]usage: bond <atom1> <atom2> [order]bond: Argument #2 is type String must be of type: [atom]usage: bond <atom1> <atom2> [order]bond: Argument #2 is type String must be of type: [atom]usage: bond <atom1> <atom2> [order] (using default radius 1.500000 for OXT) (using default radius 1.500000 for CA) (using default radius 1.500000 for C1) (using default radius 1.500000 for O1A) (using default radius 1.500000 for O1B) (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 N5) (using default radius 1.500000 for C10) (using default radius 1.500000 for O10) (using default radius 1.500000 for C11) (using default radius 1.500000 for C6) (using default radius 1.500000 for C7) (using default radius 1.500000 for O7) (using default radius 1.500000 for C8) (using default radius 1.500000 for C9) (using default radius 1.500000 for C81) (using default radius 1.500000 for C82) (using default radius 1.500000 for C91) (using default radius 1.500000 for N4) Solute vdw bounding box: 57.502 57.677 61.240 Total bounding box for atom centers: 77.502 77.677 81.240 Solvent unit box: 18.774 18.774 18.774 (using default radius 1.500000 for OXT) (using default radius 1.500000 for CA) (using default radius 1.500000 for C1) (using default radius 1.500000 for O1A) (using default radius 1.500000 for O1B) (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 N5) (using default radius 1.500000 for C10) (using default radius 1.500000 for O10) (using default radius 1.500000 for C11) (using default radius 1.500000 for C6) (using default radius 1.500000 for C7) (using default radius 1.500000 for O7) (using default radius 1.500000 for C8) (using default radius 1.500000 for C9) (using default radius 1.500000 for C81) (using default radius 1.500000 for C82) (using default radius 1.500000 for C91) (using default radius 1.500000 for N4) Total vdw box size: 80.756 81.019 84.432 angstroms. Volume: 552415.997 A^3 Mass > 274487.606 amu, Density > 0.825 g/cc (type - hence mass - of one or more atoms could not be found) Added 12722 residues.3 Na+ ions required to neutralize.Using default radius 1.50 for ion Na+Adding 3 counter ions to "comp" using 1A gridUsed default radius 1.50 for 22 atomsGrid extends from solute vdw + 1.50 to 7.50Resolution: 1.00 Angstrom.grid build: 1 secSolvent present: replacing closest with ion when steric overlaps occurCalculating grid chargescharges: 9 sec(Replacing solvent molecule)Placed Na+ in comp at (-22.85, 22.75, 4.56).(No solvent overlap)Placed Na+ in comp at (19.11, -6.61, -17.97).(Replacing solvent molecule)Placed Na+ in comp at (5.85, 31.42, 8.49).Done adding ions.Building topology.Building atom parameters.Checking Unit.FATAL: Atom .R<ILE 467>.A<OXT 20> does not have a type.FATAL: Atom .R<CA 468>.A<CA 1> does not have a type.FATAL: Atom .R<G39 469>.A<C1 1> does not have a type.FATAL: Atom .R<G39 469>.A<O1A 2> does not have a type.FATAL: Atom .R<G39 469>.A<O1B 3> does not have a type.FATAL: Atom .R<G39 469>.A<C2 4> does not have a type.FATAL: Atom .R<G39 469>.A<C3 5> does not have a type.FATAL: Atom .R<G39 469>.A<C4 6> does not have a type.FATAL: Atom .R<G39 469>.A<C5 7> does not have a type.FATAL: Atom .R<G39 469>.A<N5 8> does not have a type.FATAL: Atom .R<G39 469>.A<C10 9> does not have a type.FATAL: Atom .R<G39 469>.A<O10 10> does not have a type.FATAL: Atom .R<G39 469>.A<C11 11> does not have a type.FATAL: Atom .R<G39 469>.A<C6 12> does not have a type.FATAL: Atom .R<G39 469>.A<C7 13> does not have a type.FATAL: Atom .R<G39 469>.A<O7 14> does not have a type.FATAL: Atom .R<G39 469>.A<C8 15> does not have a type.FATAL: Atom .R<G39 469>.A<C9 16> does not have a type.FATAL: Atom .R<G39 469>.A<C81 17> does not have a type.FATAL: Atom .R<G39 469>.A<C82 18> does not have a type.FATAL: Atom .R<G39 469>.A<C91 19> does not have a type.FATAL: Atom .R<G39 469>.A<N4 20> does not have a type.Failed to generate parametersParameter file was not saved. Quit
The ligand, G39, is numbered 800 in the original pdb file, but leap seemed to renumber it as 469. Except the difference in G39 numbering, I cannot find any other thing that cause the errors, Could you help me figure it out? Thanks in advance.
Yeping Sun
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Received on Thu Jun 27 2013 - 12:00:03 PDT
