[gmx-users] problems with editconf 4.0

[Jochen Hub]

Hey Alan,

I think there is a litle bug in editconf. If you add a CRYST1 line with
some random numbers into the first Complex.pdb, editconf works fine adds
the corret CRYST1 line according to your option (-d and -bt).

Best, Jochen

Alan wrote:
> Hello,
> So this command used to work fine:
> 
> editconf -bt triclinic -f Complex.pdb -o Complex.pdb -d 1.0
> 
> Now, with gmx 4.0 (from fink for Mac Intel Leopard), I got a warning:
> 
> WARNING: No boxtype specified - distance condition applied in each
> dimension.
> 
> (no box information is inserted in the pdb file as it used to do in gmx 3)
> 
> and then when I try:
> 
> genbox -cp Complex.pdb -cs ffamber_tip3p.gro -o Complex_b4ion.pdb -p Complex.top
> 
> I get this error:
> 
> -------------------------------------------------------
> Program genbox, VERSION 4.0
> Source code file: gmx_genbox.c, line: 744
> 
> Fatal error:
> Undefined solute box.
> Create one with editconf or give explicit -box command line option
> -------------------------------------------------------
> 
> If I change '-o Complex.pdb' to '-o Complex.gro' and so on (i.e, if I use
> gro instead of pdb), all work fine.
> 
> So, pdb format is not ok anymore with gmx commands or there's a bug here?
> 
> Many thanks in advance,
> Alan
> 
> 
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-- 
************************************************
Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312
************************************************