I'm not sure, I can imagine that someone would have programmed it to do
that. Might aswell try that first and if the error persists go back and
add the chain IDs.
On Fri, Mar 2, 2012 at 2:22 AM, kanika sharma <ksharma997.gmail.com> wrote:
> Adding "TER" after OXT of first monomer should serve the purpose i guess.
> If i add TER and there is no chain identifiers for both the units in the
> file, Will LEaP be able to distinguish between them?
>
> On Fri, Mar 2, 2012 at 12:43 PM, Aron Broom <broomsday.gmail.com> wrote:
>
> > Your PDB has two identical copies of some monomeric protein, but they
> don't
> > have unique chain IDs. So LEaP thinks it is all one molecule, and is
> > trying to bond the C-terminus of the first one to the N-terminus of the
> > second. Also, the second copy may have some kind of backbone problems,
> > missing atoms or something, I didn't look carefully though, but rendering
> > the backbone is giving trouble.
> >
> > If you don't need both copies, just delete the second one from the pdb
> and
> > go from there. If you need both, you need to download a pdb from the
> RCSB
> > and see which column the chain identifier is in, and then add say "A" for
> > the first copy and "B" for the second copy. You might also add a line
> > after each monomer with the "TER" keyword such that LEaP knows that chain
> > has ended.
> >
> > ~Aron
> >
> > On Fri, Mar 2, 2012 at 1:59 AM, kanika sharma <ksharma997.gmail.com>
> > wrote:
> >
> > > Hi Amber list,
> > >
> > > I am trying to work with my protein using Leap but when I try to create
> > the
> > > top and crd files, I get the message
> > >
> > > > saveamberparm var 40_240.top 40_240.crd
> > > Checking Unit.
> > > WARNING: There is a bond of 38.732284 angstroms between:
> > > ------- .R<ALA 81>.A<C 9> and .R<THR 82>.A<N 1>
> > > FATAL: Atom .R<ALA 81>.A<OXT 11> does not have a type.
> > > Failed to generate parameters
> > > Parameter file was not saved.
> > >
> > >
> > > I am using the ff99SB forcefield, and I used the saveamberparm command.
> > Any
> > > advice on getting Leap to work with my file?
> > >
> > > Here is the file attached
> > >
> > > _______________________________________________
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> > >
> > >
> >
> >
> > --
> > Aron Broom M.Sc
> > PhD Student
> > Department of Chemistry
> > University of Waterloo
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Fri Mar 02 2012 - 00:00:02 PST
