From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Jun 01 2012 - 02:39:56 CDT
Hi
If you use binaryrestart no, the restart files are already pdb.
Also the catdcd tool can produce pdb files of selected frames from a dcd
file.
Regards
Norman
> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Nicholas M Glykos
> Gesendet: Freitag, 1. Juni 2012 09:18
> An: Ajith Rathnaweera Rajapaksha Mudalige
> Cc: namd-l_at_ks.uiuc.edu
> Betreff: Re: namd-l: Writing an output file into pdb format in a
> simulation.
>
>
>
>
> > I am in need to write an output file in pdb format at the stage of
> > simulation in progress.
>
>
> catdcd4 -o selected_frame.dcd -first 20040 -last 20040 now_running.dcd
>
> and then use vmd to convert selected_frame.dcd to pdb format.
>
>
> Or, if you have carma installed (and a PSF file) :
>
> carma -v -pdb -atmid ALLID -first 20040 -last 20040 now_running.dcd
> my.psf
>
>
>
>
> --
>
>
> Nicholas M. Glykos, Department of Molecular Biology
> and Genetics, Democritus University of Thrace, University Campus,
> Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office)
> +302551030620,
> Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/
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