[gmx-users] genbox error at futil.c

iulek iulek at interponta.com.br
Tue Jun 23 16:19:59 CEST 2009

    Thanks for replying.

    Humm..., maybe I see now. As a beginner I intended to keep all files 
produced and better inspect what happens in sequence, but I did not want 
to use the conventional renaming. But it seems that for the topology 
file, the common procedure is to keep always one only name through the 
several steps, right? That is what I understand with

Option     Filename  Type         Description
  -p      topol.top  In/Out, Opt. Topology file

    so, the same name for input and output, yet genbox renames the old 
one according to the conventions (which in my script I could then 
further "re-rename").
    And... genbox does need a previous topology file (RecA_nat_b4em.top 
was intended to be the output file!).
    Thanks, again.


> iulek wrote:
>> Hi!
>>     I am a very beginner, trying to make some dynamics of a protein 
>> in a water box, after doing some (web) tutorials. I googled first for 
>> this (possibly simple) error, found one reference, but cannot see it, 
>> possibly because the gromacs site is under changes.
>>     I ran pdb2gmx and editconf. Then at genbox I get the error:
>> "
>> Processing topology
>> -------------------------------------------------------
>> Program genbox, VERSION 4.0.5
>> Source code file: futil.c, line: 330
>> File input/output error:
>> RecA_nat_b4em.top
>> -------------------------------------------------------
>> "
> So is the topology in the current working directory?
> -Justin
>>     The command line is:
>>  > genbox -cp ${MOL}_in_box.gro -cs -p ${MOL}_b4em.top -o 
>> ${MOL}_b4em.gro << eof > genbox.log
>> eof
>>     with variable MOL set to RecA_nat
>>     The file RecA_nat_b4em.gro is output without problems.
>>     I am using gromacs 4.0.5 under openSuSE 11.1.
>>     Thanks,
>> Jorge
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