Re: [AMBER] Error in prmtop and inpcrd atom

From: somdev pahari <somdevpahari1.gmail.com>
Date: Tue, 9 Jul 2019 10:24:36 +0530

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 12, which is extremely out of date.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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Received on Mon Jul 08 2019 - 22:00:02 PDT
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