[gmx-users] gromacs 4.6.1 installation problem

[Roshan Shrestha]

I am about to burst into tears now, since I am unable to get in touch with
you guys. My problem is regarding the installation of gromacs 4.6.1, I
followed exactly what was said in
https://rohitnarurkar.wordpress.com/2013/08/26/gromacs-installation-for-linux-users/
I followed with success till the last one,but when I typed grompp, it
showed error like Program grompp, VERSION 4.6.1 Source code file:
/home/roshan2004/Downloads/gromacs-4.6.1/src/gmxlib/futil.c, line: 593
File input/output error: grompp.mdp For more information and tips for
troubleshooting, please check the GROMACS website at
http://www.gromacs.org/Documentation/Errors with some information about
gromacs above, when I typed which mdrun Program mdrun, VERSION 4.6.1 Source
code file: /home/roshan2004/Downloads/gromacs-4.6.1/src/gmxlib/gmxfio.c,
line: 524
Can not open file: topol.tpr For more information and tips for
troubleshooting, please check the GROMACS website at
http://www.gromacs.org/Documentation/Errors So, clearly, there are some
errors, Now, how to fix this ?

[Jordan Wolfson]

Dear Roshan,

Don't let it get to you! Gromacs is frustrating for all people relatively
new. Sorry I can't help with your problem as I am not exactly an expert
here but I am trying to provide moral support: hang in there! People are
very helpful in the gromacs community and I am sure you will be able to
figure out your problem sooner or later.

P.S. If I can see your email I am sure an expert will be able to provide
you with help for your problem sooner or later. Don't give up!

Sincerely,

Jordan Wolfson

Post by Roshan Shrestha
I am about to burst into tears now, since I am unable to get in touch with
you guys. My problem is regarding the installation of gromacs 4.6.1, I
followed exactly what was said in
https://rohitnarurkar.wordpress.com/2013/08/26/gromacs-installation-for-linux-users/
I followed with success till the last one,but when I typed grompp, it
/home/roshan2004/Downloads/gromacs-4.6.1/src/gmxlib/futil.c, line: 593
File input/output error: grompp.mdp For more information and tips for
troubleshooting, please check the GROMACS website at
http://www.gromacs.org/Documentation/Errors with some information about
gromacs above, when I typed which mdrun Program mdrun, VERSION 4.6.1 Source
code file: /home/roshan2004/Downloads/gromacs-4.6.1/src/gmxlib/gmxfio.c,
line: 524
Can not open file: topol.tpr For more information and tips for
troubleshooting, please check the GROMACS website at
http://www.gromacs.org/Documentation/Errors So, clearly, there are some
errors, Now, how to fix this ?
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or

[Justin Lemkul]

Post by Roshan Shrestha
I am about to burst into tears now, since I am unable to get in touch with
you guys. My problem is regarding the installation of gromacs 4.6.1, I
followed exactly what was said in
https://rohitnarurkar.wordpress.com/2013/08/26/gromacs-installation-for-linux-users/
I followed with success till the last one,but when I typed grompp, it
/home/roshan2004/Downloads/gromacs-4.6.1/src/gmxlib/futil.c, line: 593
File input/output error: grompp.mdp For more information and tips for
troubleshooting, please check the GROMACS website at
http://www.gromacs.org/Documentation/Errors with some information about
gromacs above, when I typed which mdrun Program mdrun, VERSION 4.6.1 Source
code file: /home/roshan2004/Downloads/gromacs-4.6.1/src/gmxlib/gmxfio.c,
line: 524
Can not open file: topol.tpr For more information and tips for
troubleshooting, please check the GROMACS website at
http://www.gromacs.org/Documentation/Errors So, clearly, there are some
errors, Now, how to fix this ?

If you simply type 'grompp' or 'mdrun' with no arguments, it tries to run the
program using default file names. That's all the errors above indicate.
There's nothing wrong with the installation.

Note that 4.6.1 is positively ancient and it is strongly advised that you
upgrade to the latest release (5.1) for doing any new science.

-Justin
--
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

***@outerbanks.umaryland.edu | [phone]
http://mackerell.umaryland.edu/~jalemkul

==================================================