Dear David,
thanks for suggestions again.
One question: what should I do with the non-integer charges (below you can
see warning obtained for my solvated system?)
WARNING: The unperturbed charge of the unit: -2.998000 is not zero.
In this case -2 charge came from the protein and ligand should have -1 as
defined during its parametrization:
antechamber -i ligand.pdb -fi pdb -o ligand.mol2 -fo mol2 -c bcc -s 2 -nc -1
but in fact obtaining ligand -0.998000 I've obtained some problems with the
neutralization of my system (See below ). Should I use another charge
assignment method for my ligand?
> addions complex Na+ 0
2 Na+ ions required to neutralize.
Adding 2 counter ions to "complex" using 1A grid
Grid extends from solute vdw + 1.87 to 7.97
Resolution: 1.00 Angstrom.
grid build: 0 sec
Solvent present: replacing closest with ion
when steric overlaps occur
Calculating grid charges
charges: 3 sec
(Replacing solvent molecule)
Placed Na+ in complex at (-19.80, 1.13, 3.10).
(Replacing solvent molecule)
Placed Na+ in complex at (5.02, -5.38, 5.14).
Done adding ions.
> check complex
Checking 'complex'....
WARNING: The unperturbed charge of the unit: -0.998000 is not zero.
James
2014-04-29 21:12 GMT+04:00 David A Case <case.biomaps.rutgers.edu>:
> On Tue, Apr 29, 2014, James Starlight wrote:
> >
> > E.g using below script I've loaded my complex.pdb
> >
> > source leaprc.ff99SB
> > source leaprc.gaff
> > complex = complex.pdb
>
> > check complex
> > resulted in the 34 errors (corresponded to the ligand atoms) indicating
> > that ligand parameters have not been loaded.
>
> Indeed. You need to load the ligand .off or .mol2 file (that defines its
> topology), plus and frcmod files you need for the ligand. This has nothing
> to do with whether you solvate things or not.
>
> Maybe I am not understanding your question, however. Don't be afraid to
> experiment!
>
> ...dac
>
>
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Received on Tue Apr 29 2014 - 12:00:02 PDT
