mohit kumar wrote:
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...
Use sftp.
-Justin
thnx again..for your help!!
On Sun, Jul 12, 2009 at 9:01 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> 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
<[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>> 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
<[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>
<mailto:[email protected] <mailto:[email protected]>
<mailto:[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> <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> <http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list [email protected]
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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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list [email protected]
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Please search the archive at http://www.gromacs.org/search before
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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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