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 <[email protected]
<mailto:[email protected]>> 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> | (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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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