[gmx-users] spider toxin tutorial problem
Justin A. Lemkul
jalemkul at vt.edu
Mon Jul 13 04:29:37 CEST 2009
mohit kumar wrote:
> ok.thanx very much .......so but it happens generally to all tutorials i
> have done..means...grompp not able to find .gro files....i have tried
> 3-4 tutorial..and i stuck at same place everytime. please tell me how to
> download coordinate files...
Use sftp.
-Justin
> thnx again..for your help!!
>
> On Sun, Jul 12, 2009 at 9:01 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> 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>
> <mailto: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>>
> <mailto: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>
> <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> <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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