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 <jalem...@vt.edu
<mailto:jalem...@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 <jalem...@vt.edu
<mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@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>>
==============================____==========
--
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
http://lists.gromacs.org/____mailman/listinfo/gmx-users
<http://lists.gromacs.org/__mailman/listinfo/gmx-users>
<http://lists.gromacs.org/__mailman/listinfo/gmx-users
<http://lists.gromacs.org/mailman/listinfo/gmx-users>>
Please search the archive at
http://www.gromacs.org/____Support/Mailing_Lists/Search
<http://www.gromacs.org/__Support/Mailing_Lists/Search>
<http://www.gromacs.org/__Support/Mailing_Lists/Search
<http://www.gromacs.org/Support/Mailing_Lists/Search>> before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface
or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-request@__gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>.
Can't post? Read http://www.gromacs.org/____Support/Mailing_Lists
<http://www.gromacs.org/__Support/Mailing_Lists>
<http://www.gromacs.org/__Support/Mailing_Lists
<http://www.gromacs.org/Support/Mailing_Lists>>
--
==============================__==========
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>
==============================__==========
--
gmx-users mailing list gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/__mailman/listinfo/gmx-users
<http://lists.gromacs.org/mailman/listinfo/gmx-users>
Please search the archive at
http://www.gromacs.org/__Support/Mailing_Lists/Search
<http://www.gromacs.org/Support/Mailing_Lists/Search> before posting!
Please don't post (un)subscribe requests to the list. Use the www interface
or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
<http://www.gromacs.org/Support/Mailing_Lists>
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
