On Mon, Jul 8, 2019 at 3:41 AM shivangi agarwal
<shiviagarwalpharma.gmail.com> wrote:
>
> 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.
Did you follow the advice previously given to you and try AmberTools
19, read chapter 3, etc? Your output still shows you as using Amber
12, which is extremely out of date. It also shows a warning at the
very beginning (about assigned bond types being wrong). Have you
attempted to look into this? How did you generate ligand2.pdb?
The tutorial you are following is categorized as advanced. I highly
recommend that you try to complete some of the basic tutorials first
so you can get a better feel for what antechamber/leap are trying to
do, which in turn will give you the tools to better troubleshoot these
issues.
-Dan
>
>
> 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 - 06:30:05 PDT
