Re: [AMBER] top and crd file error

From: Aron Broom <>
Date: Fri, 2 Mar 2012 02:13:01 -0500

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.


On Fri, Mar 2, 2012 at 1:59 AM, kanika sharma <> 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.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
> _______________________________________________
> AMBER mailing list

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
AMBER mailing list
Received on Thu Mar 01 2012 - 23:30:02 PST
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