[gmx-users] spider toxin tutorial problem
mohit kumar
sahajmohit at gmail.com
Mon Jul 13 04:27:04 CEST 2009
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...
thnx again..for your help!!
On Sun, Jul 12, 2009 at 9:01 PM, Justin A. Lemkul <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>> 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
>>
>> ========================================
>> _______________________________________________
>> 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
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>> 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
>
> ========================================
> _______________________________________________
> gmx-users mailing list 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.
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>
--
MOHIT KUMAR
Molecular Biochemistry & Biophysics
Graduate Student
Illinois Institute of Technology
Chicago,IL, USA
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