From: flavio seixas (oivalf_nix_at_yahoo.com)
Date: Thu Dec 12 2013 - 16:22:45 CST

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