Dear sir
I have followed this tutorial (ion recognition in leap,
http://ambermd.org/tutorials/advanced/tutorial20/nonbonded_model.htm) and
have generated atomic_ions.lib file. But it is still showing error as:
For atom: .R<ZN 260>.A<ZN 1> Could not find type: Zn2+
Parameter file was not saved.
Hereby, i am attaching my terminal commands which I have given.
Please go through the commands and suggest me a possible solution to come
out of this error.
Thanks and regards
Shivangi Agarwal
On Wed, Jul 3, 2019 at 11:15 PM David Case <david.case.rutgers.edu> wrote:
> On Wed, Jul 03, 2019, shivangi agarwal wrote:
>
> > For atom: .R<ZN 260>.A<ZN 1> Could not find type: Zn2+
> >
> >*antechamber -i ligand.pdb -fi pdb -o ligand.mol2 -fo mol2 -c bcc -s
> >2parmchk -i ligand.mol2 -f mol2 -o ligand.frcmodtleapsource
> >leaprc.ff99SBsource leaprc.gaffLIG=loadmol2 ligand.mol2listcheck
> >LIGloadamberparams ligand.frcmodsaveoff LIG ligand.libsaveamberparm LIG
> >ligand.prmtop ligand.inpcrdquittleap -s -f Zn.intleapsource
> >leaprc.ff99SBsource leaprc.gaffloadamberparams ligand.frcmodloadoff
> >atomic_ions.libloadoff ligand.libcomplex =loadpdb rec_lig.pdbsaveamberparm
> >complex rec_lig.prmtop rec_lig.inpcrdsavepdb complex rec_lig.pdb*
>
> Your email program (or maybe mine?) has made it very hard to read the
> above. But it looks like you are using a very old version of
> AmberTools, since we have not had a "leaprc.ff99SB" in the search path
> for many years. I suspect that you are never loading the parameters for
> ions like zinc.
>
> I think you are going to have to download AmberTools19, and read Chapter
> 3 about how force fields are loaded. You can keep your old ligand.*
> files. The default approach will treat interactions between zinc and
> other atoms as non-bonded ones. You'll have to see if this meets your
> needs. If not, consult sections 15.7 and 15.8 in the manual, which
> discusses ways to handle metals.
>
> ...good luck....dac
>
>
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Received on Mon Jul 08 2019 - 01:00:02 PDT
