AMBER Archive (2003)

Subject: Re: ptraj generated PDB files

From: caldwell_at_heimdal.compchem.ucsf.edu
Date: Fri May 16 2003 - 08:07:57 CDT

That's not a ptraj "problem", but rather a function of how leap builds
topology files from the residue database. If you want to compare your
initial structure 1 to 1 against the ptraj file, do a "savePDB" in
leap to get your structure in the "amber" order.

jim

On Fri, 16 May 2003, Fabian Boes wrote:

> hello ...
>
> ... i've noticed that in a ptraj generated pdb file the order of the atoms for each residue are a little bit different then in the original pdb file from the database. the C and O atoms appear at the end of the residue. is this known to others? any solution how to get the atoms in the "right" order like in the original pdb file?
>
> ptraj generated:
>
> ATOM 49 N LYS
> ATOM 50 CA LYS
> ATOM 51 CB LYS
> ATOM 52 CG LYS
> ATOM 53 CD LYS
> ATOM 54 CE LYS
> ATOM 55 NZ LYS
> ATOM 56 C LYS <----
> ATOM 57 O LYS <----
>
> original pdb file:
>
> ATOM 49 N LYS
> ATOM 50 CA LYS
> ATOM 51 C LYS <----
> ATOM 52 O LYS <----
> ATOM 53 CB LYS
> ATOM 54 CG LYS
> ATOM 55 CD LYS
> ATOM 56 CE LYS
> ATOM 57 NZ LYS
>
> Sincerly,
>
> Fabian
>
>
>
> ---------------------------------------------------------------
> Fabian Bös
>
> Institute of Technical Biochemistry
> University of Stuttgart / Germany
>
> Phone: +49-711-6857481
> Fax: +49-711-6853196
> Email: fabian.boes_at_po.uni-stuttgart.de
>
> http://www.itb.uni-stuttgart.de
> --------------------------------------------------------------
>
>
> 

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