[gmx-users] trjconv PDB format problems (3.2.1)

[Tamas Horvath]

well, either way, it's not up to specs... but we had bigger problems :)

On 2/3/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> Tamas Horvath wrote:
> > But... it's no big deal to change HEADER to REMARK, is it?
> According to the pdb standard HEADER is obligatory, which doesn't really
> bother me in itself. However you can also do a one-liner
>
> grep -v HEADER orig.pdb > new.pdb
>
> to get rid of it...
>
> >
> > On 2/3/06, *Tamas Horvath* <hotafin at gmail.com
> > <mailto:hotafin at gmail.com>> wrote:
> >
> >     The BioJava PDB parser
> >
> >
> >     On 2/3/06, *David van der Spoel* <spoel at xray.bmc.uu.se
> >     <mailto:spoel at xray.bmc.uu.se>> wrote:
> >
> >         Tamas Horvath wrote:
> >         >  Hi!
> >         >  trjconv generates an invalid HEADER record.
> >         >
> >         >  REMARK    GENERATED BY TRJCONV
> >         >  HEADER    Protein in water t=   0.00000
> >         >  REMARK    THIS IS A SIMULATION BOX
> >         >
> >         >  According to the pdb file format specifications, it's an
> >         invalid header,
> >         >  and it causes problems while parsing.
> >         >  So, can it be changed to REMARK?
> >         >
> >         >  (Sorry if it has been changed since 3.2.1)
> >         >
> >         >
> >         >
> >
> ------------------------------------------------------------------------
> >         >
> >         >  _______________________________________________
> >         >  gmx-users mailing list     gmx-users at gromacs.org
> >         <mailto:gmx-users at gromacs.org>
> >         >  http://www.gromacs.org/mailman/listinfo/gmx-users
> >         >  Please don't post (un)subscribe requests to the list. Use the
> >         >  www interface or send it to gmx-users-request at gromacs.org
> >         <mailto:gmx-users-request at gromacs.org>.
> >         >  Can't post? Read
> >         http://www.gromacs.org/mailing_lists/users.php
> >         <http://www.gromacs.org/mailing_lists/users.php>
> >         What's wrong with it? The header should be a string of max 40
> >         characters, see
> >
> http://www.pdb.org/pdb/static.do?p=file_formats/pdb/format_guide_noframes.html
> >         <
> http://www.pdb.org/pdb/static.do?p=file_formats/pdb/format_guide_noframes.html
> >
> >
> >         What software is complaining about it?
> >
> >         --
> >         David.
> >
> ________________________________________________________________________
> >         David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics
> group,
> >         Dept. of Cell and Molecular Biology, Uppsala University.
> >         Husargatan 3, Box 596,          75124 Uppsala, Sweden
> >         phone:  46 18 471 4205          fax: 46 18 511 755
> >         spoel at xray.bmc.uu.se
> >         <mailto:spoel at xray.bmc.uu.se>    spoel at gromacs.org
> >         <mailto:spoel at gromacs.org>   http://folding.bmc.uu.se
> >
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >         _______________________________________________
> >         gmx-users mailing list    gmx-users at gromacs.org
> >         <mailto:gmx-users at gromacs.org>
> >         http://www.gromacs.org/mailman/listinfo/gmx-users
> >         Please don't post (un)subscribe requests to the list. Use the
> >         www interface or send it to gmx-users-request at gromacs.org
> >         <mailto:gmx-users-request at gromacs.org>.
> >         Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >         <http://www.gromacs.org/mailing_lists/users.php>
> >
> >
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060203/b3cb942c/attachment.html>