[gmx-users] spider toxin tutorial problem
Justin A. Lemkul
jalemkul at vt.edu
Mon Jul 13 04:01:48 CEST 2009
mohit kumar wrote:
> i write down all steps till i got stuck...my server is using 4.0.2
> version..ya fws_b4pr.gro is successfully created..someone suggest me its
> may be due to excessive charge...i dnt get that point.
>
I don't understand what "excessive charge" would be about. All the commands
work perfectly on my local machine, therefore, they should work. I would be
willing to bet that you're seeing a filesystem blip and grompp can't find your
coordinate file (either momentarily or ever). Again, I recommend downloading
the coordinate file and processing with grompp on a local machine.
-Justin
> On Sun, Jul 12, 2009 at 8:16 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> mohit kumar wrote:
>
> oh!!!!..no i mean that instead of.pdb file i used .gro
> file..from the begining...in the tutorial they dont change to
> .gro type.. but i do...and i carefully apply....i am able to run
> mdrun command for energy minimisation..and in this command i
> want output file ..so i used *-c fws_b4pr.gro*...but when i ran
> grompp for position restrained it show the error..though the
> file has been created in directory/server
>
>
> So fws_b4pr.gro was successfully created, but then grompp can't find
> it? Maybe you're seeing some sort of network/NFS problem when
> accessing the server. Do you have a local machine where you can try
> again? Otherwise, post all your commands exactly as you have
> entered them to see if anyone can spot a typo or other problem.
>
> -Justin
>
> On Sun, Jul 12, 2009 at 7:47 PM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>
>
>
> mohit kumar wrote:
>
> im trying this spider toxin tutorial as beginner ....the
> mdrun
> command after energy minimization have *-c fws_b4pr.pdb(i
> make
> .gro)* and then on page no 9 the grompp command for the
> postion
> restrained uses *-c fws_b4pr.gro* and when i run it show:
> Program grompp, VERSION 4.0.2
> Source code file: futil.c, line: 330
>
> File input/output error:
> fws_b4pr.gro
> ------------------------------
> -------------------------
>
> "Hey Man You Know, I'm Really OK" (Offspring)
> what may be the reason for this..im really confused!!!
>
>
> Probably a typo or you lack read/write permissions in the
> directory.
> Otherwise, how did you "make .gro?" Did you use editconf,
> or did
> you just rename the file?
>
> -Justin
>
>
> -- MOHIT KUMAR
> Molecular Biochemistry & Biophysics
> Graduate Student
> Illinois Institute of Technology
> Chicago,IL, USA
>
>
>
> ------------------------------------------------------------------------
>
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> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
> 231-9080
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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>
> --
> MOHIT KUMAR
> Molecular Biochemistry & Biophysics
> Graduate Student
> Illinois Institute of Technology
> Chicago,IL, USA
>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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>
>
> --
> MOHIT KUMAR
> Molecular Biochemistry & Biophysics
> Graduate Student
> Illinois Institute of Technology
> Chicago,IL, USA
>
--
========================================
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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