Thanks for your reply.
I have installed AmberTools19. When I am loading my protein _ligand_complex
file (complex loadpdb complex.pdb), it is showing error.
I am hereby attaching error message and complex.pdb
Kindly suggest.
On Tue, Jul 9, 2019 at 10:26 AM somdev pahari <somdevpahari1.gmail.com>
wrote:
> Dear Shivangi,
>
> Yes, you can install AmberTools 19 with Amber12. Here I paste a link.
> http://jswails.wikidot.com/installing-ambertools-14-and-older-amber
> Hope it will help you.
>
> Regards
> Somdev Pahari
> PhD Scholar
> NIT Rourkela
> India
>
> On Tue, Jul 9, 2019 at 9:40 AM 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 12, which is extremely out of date.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
> > > > >
> > > > >
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jul 09 2019 - 06:00:02 PDT
