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 <b>-c fws_b4pr.gro</b>...but when i ran grompp for position restrained it show the error..though the file has been created in directory/server<br>
<br><div class="gmail_quote">On Sun, Jul 12, 2009 at 7:47 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">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><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;">
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:<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>
</blockquote>
<br></div>
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?<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>
<br>
-- <br>
MOHIT KUMAR<br>
Molecular Biochemistry & Biophysics<br>
Graduate Student<br>
Illinois Institute of Technology<br>
Chicago,IL, USA<br>
<br>
<br></div>
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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>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
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</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>