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 hydrogen’s 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 Wed Sep 17 2014 - 06:30:02 PDT
