Hi Thomas,
Yes, the receptor.pdb file only contains the receptor.
Is this the correct understanding.. if I load the original receptor-ligand
complex (1WM1.pdb), with the loaded library of just the GAFF paramaterized
ligand (ptb.lib) - would leap recognise this and modify the parameters in
the 1WM1 ligand with the GAFF parameters? I've reread tutorial 4b many
times and the only reference I can find to creating the complex is this:
"In order to have the 1FKO pdb file recognized by tLeap once the Sustiva
library file is loaded, we need to change the residue name in the 1FKO pdb
file from EFZ to SUS. Since the Sustiva libary file includes the same atom
names as the Sustiva molecule in the 1FKO pdb file, no further modification
is necessary."
That seems to suggest I should be using the original receptor-ligand
complex as described above.
I'm happy to just combine the two pdb's I have now, either manually chimera
or leap (though I cannot seem to find the command to do this (unless I
create two variables with loadpdb (receptor, ligand) and then execute
`complex = combine { receptor ligand }` but I am not sure this syntax is
right. I also don't know what the appropriate step is to do this. I just
tried in chimera to import the parameterized ligand into the prepared
waterboxed receptor but the coordinates have changed and the ligand is
sitting in the water outside the receptor.
Sorry for the confusion, still quite lost here.
Sebastian
On 10 April 2013 17:53, <steinbrt.rci.rutgers.edu> wrote:
> 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
>
> _______________________________________________
> 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
Received on Wed Apr 10 2013 - 19:00:03 PDT
