VMD-L Mailing List
From: flavio seixas (oivalf_nix_at_yahoo.com)
Date: Thu Dec 12 2013 - 16:22:45 CST
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Hi Ramin,
Alternatively you can open your vmd-output.pdb file in the USC Chimera program and simply save it as chimera-output.pdb(Save as pdb).
Chimera will automatically provide the output file with all CONNECT (hetatoms file only) as well as a selection of the residues which form alpha-helices or beta-sheet(REMARKs).
Regards,
Flavio
-------------------------------------
Flavio Augusto Vicente Seixas
Laboratory of Structural Biochemistry
Department of Biochemistry
Universidade Estadual de Maringá, PR, Brazil
http://www.uem.br
________________________________
From: Axel Kohlmeyer <akohlmey_at_gmail.com>
To: Ramin Ekhteiari <ramin_ekh_at_yahoo.com>
Cc: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
Sent: Wednesday, December 11, 2013 11:21 AM
Subject: Re: vmd-l: generated pdb file via vmd
On Wed, Dec 11, 2013 at 11:26 AM, Ramin Ekhteiari <ramin_ekh_at_yahoo.com> wrote:
> I generated a pdb file from my MD trajectory ( 1 step), but When I try to
> load it via other visualize programs (e.g., maestro), I face with some
> topology problem (as my pdb file is lack of any topology data), how can I
> include the connection data into pdb file ?
PDB files typically do not contain connection data (there are CONECT
records possible, but those are meant for exceptional bonds only).
typically connection (aka topology) information for MD packages is
provided in topology files e.g. .psf. or in file formats like mol2
that contain both coordinate and topology information.
axel.
>
> Would be grateful for any advise.
>
> Cheers,
> Ramin
--
Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.
Hi Ramin,
Alternatively you can open your vmd-output.pdb file in the USC Chimera program and simply save it as chimera-output.pdb(Save as pdb).
Chimera will automatically provide the output file with all CONNECT (hetatoms file only) as well as a selection of the residues which form alpha-helices or beta-sheet(REMARKs).
Regards,
Flavio
-------------------------------------
Flavio Augusto Vicente Seixas
Laboratory of Structural Biochemistry
Department of Biochemistry
Universidade Estadual de Maringá, PR, Brazil
http://www.uem.br
- Next message: Camilo Andrés Jimenez Cruz: "HBonds representation draws bonds with atoms (Hs) not included in the selection"
- Previous message: Norman Geist: "AW: changing chain id and pdb generating"
- In reply to: Axel Kohlmeyer: "Re: generated pdb file via vmd"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]