[gmx-users] genbox error at futil.c

[Justin A. Lemkul]

iulek wrote:
>    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
> 

You can keep the same name, or manually make your own backup copies along the 
way (topol_orig.top, topol_after_sol.top, etc).

> "
> 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").

Right, genbox will not make a new file for you, it simply processes the input 
topology, which becomes the output once it is modified.

-Justin

>    And... genbox does need a previous topology file (RecA_nat_b4em.top 
> was intended to be the output file!).
>    Thanks, again.
> 
> Jorge
> 
>>
>>
>> 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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> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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