AMBER Archive (2007)

Subject: Re: AMBER: Leap adding 3 extra atoms

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Thu Jan 11 2007 - 13:33:14 CST

> Loading PDB file: ./telmi_mod.pdb
> Created a new atom named: N5 within residue: .R<TEL 298> <<<==== e.g. N5
> Created a new atom named: C35 within residue: .R<TEL 298>
> Created a new atom named: O3 within residue: .R<TEL 298>
> Added missing heavy atom: .R<TEL 298>.A<O2 60>
> Added missing heavy atom: .R<TEL 298>.A<N4 42> <<<==== e.g. N4
> Added missing heavy atom: .R<TEL 298>.A<C33 25>
> total atoms in file: 39
> Leap added 32 missing atoms according to residue templates:
> 3 Heavy
> 29 H / lone pairs
> The file contained 3 atoms not in residue templates
>
> PS: I DO NOT UNDERSTAND WHY IS IT ADDING 3 HEAVY ATOMS TO THE FILE

Notice the atom names. The names in your pdb must match the ones
in your template. Leap cannot determine that e.g. N4 in the
template is the same and N5 in your pdb.

Bill
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu