Dear Shivangi,
I guess you forgot to load corresponding leaprc file for protein . Because
once you have loaded leaprc file for protein it will recognize all the
amino acid rresidues. Hope this will work. Thanks and Regards.
Santanu Santra
On Tue, Jul 9, 2019 at 6:23 PM shivangi agarwal <
shiviagarwalpharma.gmail.com> wrote:
> 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 12, which is extremely out of date.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
> > > > > >
> > > > > >
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--
Santanu Santra
Research Scholar
Molecular Simulation Laboratory
Department of Chemistry
NIT ROURKELA
ROURKELA, 769008
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Received on Tue Jul 09 2019 - 06:00:03 PDT
