Hi,
my guess on what happened is this:
> Loading library: ./ptb.lib
this only defines the ligand unit, so that leap knows what a PTB is, it
does not automatically add it to any system you are preparing.
> Loading PDB file: ./receptor.pdb
does receptor.pdb only contain the receptor? In that case, leap builds a
system out of all atoms in the pdb, completes all residues but nothing
else.
If you want the complex, you need to provide a pdb of protein+ligand, or
explicitly combine the receptor and ligand files in leap.
Maybe this helps?
Thomas
On Tue, April 9, 2013 7:43 pm, Sebastian Petrik wrote:
> Hello again Julio (and hello Thomas),
>
> Julio, yes, I believe we met there... Seems you might be rescuing me once
> more!
> Thomas, yes, the ligand does not appear in either UCSF or Maestro.
> Investigation into the PDB file does not seem to contain the ligand
> either.
>
> The zip file has been updated, I do not know why it was corrupted but I
> have checked the new copy and it works.
>
> My procedure was to download 1WM1.pdb, split the file using Chimera into
> ligand and receptor files, done receptor.pdb by simple selection/deletion.
> Hydrogens were added to the ligand file. The result is ligand_addH.mol2
> and
> receptor.pdb accordingly.
>
> antechamber, parmchk, and tleap were run accordingly.
>
> Julio, you are correct in that I used Tutorial B4 (
> http://ambermd.org/tutorials/basic/tutorial4b/). I must admit I was a bit
> confused as to whether I should be using the original PDB file containing
> the PTB ligand, or the new receptor file for leap, but it seemed to make
> sense to use the new receptor file.
>
> If I can provide any more helpful information please let me know and I'll
> do my best to obtain it.
>
> Kind regards,
> Sebastian
>
> --------------------------------------------------
>
> antechamber -i ligand_addH.mol2 -fi mol2 -o ligand_addH_antechamber.mol2
> -fo mol2 -c bcc -s 2 -nc 1
> parmchk -i ligand_addH_antechamber.mol2 -f mol2 -o
> ligand_addH_antechamber.frcmod
> tleap -f tleap01.in (followed by `quit`)
> tleap -f tleap02.in (followed by `quit`)
>
>
> tleap01.in:
> source leaprc.gaff
> PTB = loadmol2 ligand_addH_antechamber.mol2
> check PTB
> loadamberparams ligand_addH_antechamber.frcmod
> saveoff PTB ptb.lib
> saveamberparm PTB initial_ligand.prm7 initial_ligand.rst7
>
> tleap02.in:
> source leaprc.ff99SB
> source leaprc.gaff
> loadamberparams ligand_addH_antechamber.frcmod
> loadoff ptb.lib
> complex = loadpdb receptor.pdb
> addions complex Na+ 10
> solvatebox complex TIP3PBOX 8.0
> saveamberparm complex initial_complex.prm7 initial_complex.rst7
> savepdb complex initial_complex.pdb
>
>
>
> tleap output:
> Welcome to LEaP!
> (no leaprc in search path)
> Sourcing: ./tleap01.in
> ----- Source:
> /eureka-scratch/uni/phd/docking/amber/12/amber12-openmpi//dat/leap/cmd/leaprc.gaff
> ----- Source of
> /eureka-scratch/uni/phd/docking/amber/12/amber12-openmpi//dat/leap/cmd/leaprc.gaff
> done
> Log file: ./leap.log
> Loading parameters:
> /eureka-scratch/uni/phd/docking/amber/12/amber12-openmpi//dat/leap/parm/gaff.dat
> Reading title:
> AMBER General Force Field for organic molecules (Version 1.4, March 2010)
> add. info. at the end
> Loading Mol2 file: ./ligand_addH_antechamber.mol2
> Reading MOLECULE named 1wm1.pdb
> Checking 'PTB'....
> WARNING: The unperturbed charge of the unit: 0.998001 is not zero.
> Checking parameters for unit 'PTB'.
> Checking for bond parameters.
> Checking for angle parameters.
> check: Warnings: 1
> Unit is OK.
> Loading parameters: ./ligand_addH_antechamber.frcmod
> Reading force field modification type file (frcmod)
> Reading title:
> remark goes here
> Creating ptb.lib
> Building topology.
> Building atom parameters.
> Checking Unit.
> WARNING: The unperturbed charge of the unit: 0.998001 is not zero.
>
> -- ignoring the warning.
>
> 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
>
> PTB 1
> )
> (no restraints)
>> quit
> Quit
> -I: Adding
> /eureka-scratch/uni/phd/docking/amber/12/amber12-openmpi//dat/leap/prep to
> search path.
> -I: Adding
> /eureka-scratch/uni/phd/docking/amber/12/amber12-openmpi//dat/leap/lib to
> search path.
> -I: Adding
> /eureka-scratch/uni/phd/docking/amber/12/amber12-openmpi//dat/leap/parm to
> search path.
> -I: Adding
> /eureka-scratch/uni/phd/docking/amber/12/amber12-openmpi//dat/leap/cmd to
> search path.
> -f: Source tleap02.in.
>
> Welcome to LEaP!
> (no leaprc in search path)
> Sourcing: ./tleap02.in
> ----- Source:
> /eureka-scratch/uni/phd/docking/amber/12/amber12-openmpi//dat/leap/cmd/leaprc.ff99SB
> ----- Source of
> /eureka-scratch/uni/phd/docking/amber/12/amber12-openmpi//dat/leap/cmd/leaprc.ff99SB
> done
> Log file: ./leap.log
> Loading parameters:
> /eureka-scratch/uni/phd/docking/amber/12/amber12-openmpi//dat/leap/parm/parm99.dat
> Reading title:
> PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
> incl.02/04/99
> Loading parameters:
> /eureka-scratch/uni/phd/docking/amber/12/amber12-openmpi//dat/leap/parm/frcmod.ff99SB
> Reading force field modification type file (frcmod)
> Reading title:
> Modification/update of parm99.dat (Hornak & Simmerling)
> Loading library:
> /eureka-scratch/uni/phd/docking/amber/12/amber12-openmpi//dat/leap/lib/all_nucleic94.lib
> Loading library:
> /eureka-scratch/uni/phd/docking/amber/12/amber12-openmpi//dat/leap/lib/all_amino94.lib
> Loading library:
> /eureka-scratch/uni/phd/docking/amber/12/amber12-openmpi//dat/leap/lib/all_aminoct94.lib
> Loading library:
> /eureka-scratch/uni/phd/docking/amber/12/amber12-openmpi//dat/leap/lib/all_aminont94.lib
> Loading library:
> /eureka-scratch/uni/phd/docking/amber/12/amber12-openmpi//dat/leap/lib/ions94.lib
> Loading library:
> /eureka-scratch/uni/phd/docking/amber/12/amber12-openmpi//dat/leap/lib/solvents.lib
> ----- Source:
> /eureka-scratch/uni/phd/docking/amber/12/amber12-openmpi//dat/leap/cmd/leaprc.gaff
> ----- Source of
> /eureka-scratch/uni/phd/docking/amber/12/amber12-openmpi//dat/leap/cmd/leaprc.gaff
> done
> Log file: ./leap.log
> Loading parameters:
> /eureka-scratch/uni/phd/docking/amber/12/amber12-openmpi//dat/leap/parm/gaff.dat
> Reading title:
> AMBER General Force Field for organic molecules (Version 1.4, March 2010)
> add. info. at the end
> Loading parameters: ./ligand_addH_antechamber.frcmod
> Reading force field modification type file (frcmod)
> Reading title:
> remark goes here
> Loading library: ./ptb.lib
> Loading PDB file: ./receptor.pdb
> Added missing heavy atom: .R<CGLY 316>.A<OXT 8>
> total atoms in file: 2520
> Leap added 2416 missing atoms according to residue templates:
> 1 Heavy
> 2415 H / lone pairs
> Adding 10 counter ions to "complex" using 1A grid
> Grid extends from solute vdw + 4.15 to 10.15
> Resolution: 1.00 Angstrom.
> grid build: 0 sec
> (no solvent present)
> Calculating grid charges
> charges: 17 sec
> Placed Na+ in complex at (30.43, -24.30, 5.80).
> Placed Na+ in complex at (29.43, 4.70, -29.20).
> Placed Na+ in complex at (45.43, 9.70, 8.80).
> Placed Na+ in complex at (46.43, -21.30, -3.20).
> Placed Na+ in complex at (4.43, 1.70, -32.20).
> Placed Na+ in complex at (-9.57, -1.30, -24.20).
> Placed Na+ in complex at (31.43, 11.70, -20.20).
> Placed Na+ in complex at (49.43, -12.30, -18.20).
> Placed Na+ in complex at (-2.57, 16.70, -17.20).
> Placed Na+ in complex at (30.43, -0.30, 19.80).
>
> Done adding ions.
> Solute vdw bounding box: 66.965 50.938 58.375
> Total bounding box for atom centers: 82.965 66.938 74.375
> Solvent unit box: 18.774 18.774 18.774
> Total vdw box size: 85.960 69.842 77.345 angstroms.
> Volume: 464348.268 A^3
> Total mass 229711.394 amu, Density 0.821 g/cc
> Added 10764 residues.
> Checking Unit.
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> Building improper torsion parameters.
> total 1083 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
>
> CGLY 1
> NLEU 1
> WAT 10764
> )
> (no restraints)
> Writing pdb file: initial_complex.pdb
> Converting N-terminal residue name to PDB format: NLEU -> LEU
> Converting C-terminal residue name to PDB format: CGLY -> GLY
>> quit
> Quit
>
>
>
>
> On 10 April 2013 06:13, Julio Dominguez <acheron24.hotmail.com> wrote:
>
>> Hi Sebastian,
>> Long time no see, I haven't been at the autodock forums but I assume we
>> meet there before. As mentioned before your zip file seems to be corrupt
>> thus, I cannot check what went wrong. Did you follow TUTORIAL B4:
>> Simulating a pharmaceutical compound using antechamber and the
>> Generalized
>> Amber Force Field.?
>> If so, your mistake maybe that you use a ligand file with different
>> coordinates than those of the original one, that is, the one bound as
>> determined by X-ray diffraction.
>> But give us more info, please.
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Wed Apr 10 2013 - 01:00:02 PDT
