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

[David van der Spoel]

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)
>         >
>         >
>         >
>         ------------------------------------------------------------------------
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>         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
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> 
> 
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-- 
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
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