Thank you very much for the suggestion!
Indeed the problem was in the variables in the leap script assigned to the
mol2 input files (as I understood they should be as the name of the ligand
in input mol2 file aswell as in the complex with the receptor which
provided to tleap on next step).
James
2014-09-18 15:21 GMT+04:00 Parker de Waal <Parker.deWaal.vai.org>:
> James,
>
> I would highly recommend reading through and completing the amber tutorial
> for ligand paramaterization.
> http://ambermd.org/tutorials/basic/tutorial4b/
>
>
> Looking at your leap input the following command jumps out at me: 'protein
> = loadmol2 ligand.mol2¹. In order for this to correspond with the frcmod
> and lib files, hopefully both named MOL you would need to run ŒMOL =
> loadmol2 ligand.mol2¹ and then run check MOL.
>
> I have a hunch this will fix your errors.
>
> Parker
>
> On 9/17/14, 9:02 AM, "James Starlight" <jmsstarlight.gmail.com> wrote:
>
> >Yes sure I've tried to applied parametrization of the ligand.pdb file
> >(stripped from hydrogens) produced by autodock with the tleap and its
> >produced errors that each atom type of the ligand has not been found:
> >
> >Unknown residue: MOL number: 0 type: Terminal/last
> >..relaxing end constraints to try for a dbase match
> > -no luck
> >Creating new UNIT for residue: MOL sequence: 1
> >Created a new atom named: C1 within residue: .R<MOL 1>
> >Created a new atom named: C2 within residue: .R<MOL 1>
> >Created a new atom named: C3 within residue: .R<MOL 1>
> >Created a new atom named: C4 within residue: .R<MOL 1>
> >Created a new atom named: C5 within residue: .R<MOL 1>
> >Created a new atom named: C6 within residue: .R<MOL 1>
> >Created a new atom named: H7 within residue: .R<MOL 1>
> >Created a new atom named: H8 within residue: .R<MOL 1>
> >Created a new atom named: H9 within residue: .R<MOL 1>
> >Created a new atom named: H10 within residue: .R<MOL 1>
> >Created a new atom named: H11 within residue: .R<MOL 1>
> >Created a new atom named: C12 within residue: .R<MOL 1>
> >Created a new atom named: H13 within residue: .R<MOL 1>
> >Created a new atom named: H14 within residue: .R<MOL 1>
> >Created a new atom named: O15 within residue: .R<MOL 1>
> >Created a new atom named: C16 within residue: .R<MOL 1>
> >Created a new atom named: O17 within residue: .R<MOL 1>
> >Created a new atom named: C18 within residue: .R<MOL 1>
> >Created a new atom named: H19 within residue: .R<MOL 1>
> >Created a new atom named: H20 within residue: .R<MOL 1>
> >Created a new atom named: H21 within residue: .R<MOL 1>
> > total atoms in file: 21
> > The file contained 21 atoms not in residue templates
> >Checking 'protein'....
> >FATAL: Atom .R<MOL 1>.A<C1 1> does not have a type.
> >FATAL: Atom .R<MOL 1>.A<C2 2> does not have a type.
> >FATAL: Atom .R<MOL 1>.A<C3 3> does not have a type.
> >FATAL: Atom .R<MOL 1>.A<C4 4> does not have a type.
> >FATAL: Atom .R<MOL 1>.A<C5 5> does not have a type.
> >FATAL: Atom .R<MOL 1>.A<C6 6> does not have a type.
> >FATAL: Atom .R<MOL 1>.A<H7 7> does not have a type.
> >FATAL: Atom .R<MOL 1>.A<H8 8> does not have a type.
> >FATAL: Atom .R<MOL 1>.A<H9 9> does not have a type.
> >FATAL: Atom .R<MOL 1>.A<H10 10> does not have a type.
> >FATAL: Atom .R<MOL 1>.A<H11 11> does not have a type.
> >FATAL: Atom .R<MOL 1>.A<C12 12> does not have a type.
> >FATAL: Atom .R<MOL 1>.A<H13 13> does not have a type.
> >FATAL: Atom .R<MOL 1>.A<H14 14> does not have a type.
> >FATAL: Atom .R<MOL 1>.A<O15 15> does not have a type.
> >FATAL: Atom .R<MOL 1>.A<C16 16> does not have a type.
> >FATAL: Atom .R<MOL 1>.A<O17 17> does not have a type.
> >FATAL: Atom .R<MOL 1>.A<C18 18> does not have a type.
> >FATAL: Atom .R<MOL 1>.A<H19 19> does not have a type.
> >FATAL: Atom .R<MOL 1>.A<H20 20> does not have a type.
> >FATAL: Atom .R<MOL 1>.A<H21 21> does not have a type.
> >
> >
> >here I've provided to tleap all files generated on the previous step by
> >anthechamber ( I have no such problem with the parametrization of the mol2
> >file produced by anthechamber too where I have the same naming for all the
> >atoms with the expeption of hydrogens):
> >
> ># for tleap
> >source leaprc.ff03.r1
> >source leaprc.gaff
> >loadamberparams /ligand/ligand.frcmod
> >loadoff /ligand/ligand.lib
> >#protein = loadpdb test.pdb
> >protein = loadmol2 ligand.mol2
> >check protein
> >savepdb protein test.pdb
> >quit
> >
> >James
> >
> >2014-09-17 13:40 GMT+02:00 David A Case <case.biomaps.rutgers.edu>:
> >
> >> On Wed, Sep 17, 2014, James Starlight wrote:
> >>
> >> > because (superimposed to the receptor cavity)
> >> > ligand.pdb produced by autodock have been stripped from all
> >>hydrogen¹s so
> >> > its coordinates not equal to initial ligand.mol2 . Will it possible
> >>using
> >> > amber's ligand.lib to restore full-atomic structure of the ligand
> >>based
> >> on
> >> > its (no H) coordinates obtained from docking?
> >>
> >> What went wrong when you tried this?
> >>
> >> Generally, if you are wondering how to do something in Amber, the best
> >> approach is to run some experiments to see what happens.
> >>
> >> ...dac
> >>
> >>
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Received on Thu Sep 18 2014 - 05:00:04 PDT
