[gmx-users] problem in running gromacs

Manik Mayur manik.mayur at gmail.com
Sat Feb 21 13:26:26 CET 2009

On Sat, Feb 21, 2009 at 5:01 PM, nitu sharma <sharmanitu35 at gmail.com> wrote:

> Dear all,
>                     Thanks for solving my problem  but again I have one
> more problem  when I put the pdb2gmx command it shows error like this
> "Program pdb2gmx, VERSION 3.3.2
> Source code file: futil.c, line: 345
> File input/output error:
> eiwit.pdb
>  I am downloading version 4.0.3  but why it shows 3.3.2 and what is the
> meaning of "File input/output error eiwit.pdb "

Every gromacs executable has a format in which it expects a series of input
and output files, however in most of the cases it assumes the default names,
it is always better to have your own nomenclature for files.

To know the input sequence for an executable, go through the documentation
or try running it without any option. What follows is a table mentioning the
options, default filename, type (input/output) and description. The
executable definitely expects the input/output files (except the opt. ones).
Executing with proper options will not generate such error.

Again go through the documentation and try running scripts in  <gromacs
directory>/share/tutor/ for practice.

Regarding version issue, you have to remove the older installation and
freshly install the new one.

could you please let me know  about that.
> Thank you very much in advance .
> Nitu Sharma
> Structural Biology lab
> school of life Sciences
> Jawaherlal nehru university
> New delhi,  India.
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-Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
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