[gmx-users] spider toxin tutorial problem

[Justin A. Lemkul]

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>> 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
> 
> 
>         ------------------------------------------------------------------------
> 
>         _______________________________________________
>         gmx-users mailing list    gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>
>         http://lists.gromacs.org/mailman/listinfo/gmx-users
>         Please search the archive at http://www.gromacs.org/search
>         before posting!
>         Please don't post (un)subscribe requests to the list. Use the
>         www interface or send it to gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>.
>         Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
>     -- 
>     ========================================
> 
>     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
> 
>     ========================================
>     _______________________________________________
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at http://www.gromacs.org/search before
>     posting!
>     Please don't post (un)subscribe requests to the list. Use the www
>     interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> 
> 
> -- 
> 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

========================================