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
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Received on Thu Mar 01 2012 - 23:30:02 PST
