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
>
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Received on Tue Apr 09 2013 - 17:00:03 PDT
