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...<br>
thnx again..for your help!!<br><br><div class="gmail_quote">On Sun, Jul 12, 2009 at 9:01 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
<br>
mohit kumar wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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.<br>
<br>
</blockquote>
<br></div>
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.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
On Sun, Jul 12, 2009 at 8:16 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
mohit kumar wrote:<br>
<br>
oh!!!!..no i mean that instead of.pdb file i used .gro<br>
file..from the begining...in the tutorial they dont change to<br>
.gro type.. but i do...and i carefully apply....i am able to run<br>
mdrun command for energy minimisation..and in this command i<br>
want output file ..so i used *-c fws_b4pr.gro*...but when i ran<br>
grompp for position restrained it show the error..though the<br>
file has been created in directory/server<br>
<br>
<br>
So fws_b4pr.gro was successfully created, but then grompp can't find<br>
it? Maybe you're seeing some sort of network/NFS problem when<br>
accessing the server. Do you have a local machine where you can try<br>
again? Otherwise, post all your commands exactly as you have<br>
entered them to see if anyone can spot a typo or other problem.<br>
<br>
-Justin<br>
<br>
On Sun, Jul 12, 2009 at 7:47 PM, Justin A. Lemkul<br>
<<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br></div><div><div></div><div class="h5">
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>> wrote:<br>
<br>
<br>
<br>
mohit kumar wrote:<br>
<br>
im trying this spider toxin tutorial as beginner ....the<br>
mdrun<br>
command after energy minimization have *-c fws_b4pr.pdb(i<br>
make<br>
.gro)* and then on page no 9 the grompp command for the<br>
postion<br>
restrained uses *-c fws_b4pr.gro* and when i run it show:<br>
Program grompp, VERSION 4.0.2<br>
Source code file: futil.c, line: 330<br>
<br>
File input/output error:<br>
fws_b4pr.gro<br>
------------------------------<br>
-------------------------<br>
<br>
"Hey Man You Know, I'm Really OK" (Offspring)<br>
what may be the reason for this..im really confused!!!<br>
<br>
<br>
Probably a typo or you lack read/write permissions in the<br>
directory.<br>
Otherwise, how did you "make .gro?" Did you use editconf,<br>
or did<br>
you just rename the file?<br>
<br>
-Justin<br>
<br>
<br>
-- MOHIT KUMAR<br>
Molecular Biochemistry & Biophysics<br>
Graduate Student<br>
Illinois Institute of Technology<br>
Chicago,IL, USA<br>
<br>
<br>
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-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540)<div class="im">
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<br>
-- MOHIT KUMAR<br>
Molecular Biochemistry & Biophysics<br>
Graduate Student<br>
Illinois Institute of Technology<br>
Chicago,IL, USA<br>
<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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<br>
-- <br>
MOHIT KUMAR<br>
Molecular Biochemistry & Biophysics<br>
Graduate Student<br>
Illinois Institute of Technology<br>
Chicago,IL, USA<br>
<br>
</div></div></blockquote><div><div></div><div class="h5">
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>MOHIT KUMAR<br>Molecular Biochemistry & Biophysics<br>Graduate Student<br>Illinois Institute of Technology<br>Chicago,IL, USA<br><br>