I have downloaded AmberTools 19. Will the same license key work for
AmberTools 19 as for Amber12?.
Regards
Shivangi
On Mon, Jul 8, 2019 at 6:58 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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 12, which is extremely out of date.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 - 21:30:02 PDT
