[gmx-users] input/output error in production grompp
Justin A. Lemkul
jalemkul at vt.edu
Wed Jun 13 15:14:12 CEST 2012
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
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.
> 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:
> 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:
> Program grompp, VERSION 4.5.4
> Source code file: futil.c, line: 491
> File input/output error:
> For more information and tips for troubleshooting, please check the GROMACS
> website at 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 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>
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Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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