AMBER Archive (2005)

Subject: Re: AMBER: leap question

From: David A. Case (case_at_scripps.edu)
Date: Fri Aug 05 2005 - 17:34:39 CDT

On Fri, Aug 05, 2005, Kara Di Giorgio wrote:

> Created a new atom named: C4 within residue: .R<Ni 13>

As Amber error messages go, this is pretty specific: the pdb file appears to
have an atom named "C4" in a residue named "Ni". You will have to hand-edit
your pdb file to get atom C4 to be in residue NCH (I assume).

> Added missing heavy atom: .R<NCH 14>.A<N1 8>

Similarly, the residue named "NCH" in the pdb file appears to be missing an
atom called "N1", which it is supposed to have. The "Ni" and "NCH" residues
in the pdb file have to have exactly the same atoms (no more, no less) than
what are in the prep files with the same name. You simply have to learn how
to fix problems like this yourself: there is no practical way that people on
the mailing list can really do it on your behalf.

...good luck...dac

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