[gmx-users] spider toxin tutorial problem

[mohit kumar]

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

On Sun, Jul 12, 2009 at 7:47 PM, Justin A. Lemkul <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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>>
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>
> --
> ========================================
>
> 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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-- 
MOHIT KUMAR
Molecular Biochemistry & Biophysics
Graduate Student
Illinois Institute of Technology
Chicago,IL, USA
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