[gmx-users] input/output error in production grompp

[Malai]

HI Justin,

I did use the .pdb file as I showed in the grompp command. If I got I/O
error, the mdrun should not work? but here the mdrun is working. Thanks.

On Wed, Jun 13, 2012 at 9:14 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/13/12 9:11 AM, Malai wrote:
>
>> Hello Justin,
>>
>> Thanks for reply. After getting this, I started to run production run but
>> here i
>> didnt get any error. so is it OK? or still I need to look at this error?
>> Thanks
>>
>>
> What's anomalous to me is that grompp produced an I/O error (referencing
> an unused or nonexistent file) but still produced a .tpr file.  Fatal
> errors prevent grompp from working, so you shouldn't have gotten a .tpr
> file in this case.
>
> You need coordinates in the .tpr file to work, but if you did in fact use
> a .pdb file, then the .tpr is fine.  The reference to the .gro file is
> still a complete mystery to me.
>
> -Justin
>
>  On Wed, Jun 13, 2012 at 8:35 PM, Justin A. Lemkul <jalemkul at vt.edu
>> <mailto:jalemkul at vt.edu>> wrote:
>>
>>
>>
>>    On 6/13/12 8:27 AM, Malai wrote:
>>
>>        HI,
>>
>>        Sorry for wrongly typing. The command I issued is:  grompp -v -f
>> hex1.mdp -c
>>        hex1.pdb -p hex1.top -o hex1.tpr.
>>
>>        The error is bellow:
>>
>>
>>        Error:
>>        Program grompp, VERSION 4.5.4
>>        Source code file: futil.c, line: 491
>>
>>        File input/output error:
>>        hex1.gro
>>        For more information and tips for troubleshooting, please check
>> the GROMACS
>>        website at http://www.gromacs.org/____**Documentation/Errors<http://www.gromacs.org/____Documentation/Errors>
>>        <http://www.gromacs.org/__**Documentation/Errors<http://www.gromacs.org/__Documentation/Errors>
>> >
>>
>>        <http://www.gromacs.org/__**Documentation/Errors<http://www.gromacs.org/__Documentation/Errors>
>>        <http://www.gromacs.org/**Documentation/Errors<http://www.gromacs.org/Documentation/Errors>
>> >>
>>
>>
>>    Even with the corrected command, I see no way for this error to come
>> up.
>>      There is no reference to a .gro file anywhere in your command.
>>
>>
>>    -Justin
>>
>>    --
>>    ==============================**__==========
>>
>>
>>    Justin A. Lemkul, Ph.D.
>>    Research Scientist
>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080<tel:%28540%29%20231-9080>
>>    http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>>    <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> >
>>
>>    ==============================**__==========
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> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
>
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