AMBER Archive (2005)

Subject: RE: AMBER: missing residue

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Mar 28 2005 - 10:23:47 CST

Dear Xueping

> WARNING: There is a bond of 75.141750 angstroms
> between:
> ------- .R<NMET 1>.A<C 18> and .R<ALA 2>.A<N 1>

Do you perhaps need a TER card between these two residues? If they are not
part of the same amino acid chain then you will need a TER card otherwise
xleap will join the C and N terminus of the two residues together. If they
are supposed to be part of the same chain then you either have the position
of one of them very wrong (check the coordinates carefully) or you have not
added the extra residue in the order it is bonded in the peptide chain.
Residues need to be specified in the same order as they are bound since Leap
will read through the pdb file bonding each residue to its two neighbours in
the order they appear in the pdb file.

I hope this helps.
All the best
Ross

/\
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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
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