To use AmberTools19 you do not need any license key. Just compile and use
it. However you will need Amber18 to use PMEMD and its cuda variants.
On Tuesday, July 9, 2019, shivangi agarwal <shiviagarwalpharma.gmail.com>
wrote:
> 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 12, which is extremely out of date.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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--
Best Regards
Elvis Martis
Mumbai.
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Received on Mon Jul 08 2019 - 22:00:02 PDT
