[gmx-users] input/output error in production grompp
Justin A. Lemkul
jalemkul at vt.edu
Wed Jun 13 15:24:09 CEST 2012
On 6/13/12 9:22 AM, Malai wrote:
> 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.
>
As I said before, if the .tpr file was produced, there was no problem. The
error message makes no sense at all to me.
-Justin
> On Wed, Jun 13, 2012 at 9:14 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto: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>
> <mailto: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> <http://vt.edu> | (540) 231-9080
> <tel:%28540%29%20231-9080> <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 <http://vt.edu> | (540) 231-9080 <tel:%28540%29%20231-9080>
> 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
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