[gmx-users] cannot generate .top file

Kwee Hong joyssstan0202 at gmail.com
Wed Oct 29 04:54:40 CET 2008

Hi. Thanks for your enlightenment. Now, I'm able to run pdb2gmx with the
output files produced. I just added 'sudo' before ./pdb2gmx and it allows me
to write in the directory. But unfortunately, this step seem does not work
for ./gmxtest.pl. I'm having the same output even after i had added 'sudo'
in front of it.

On Fri, Oct 24, 2008 at 8:52 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> Kwee Hong wrote:
>> Hi.
>> I seem having some problem in running ./pdb2gmx. Here is the output file.
>> Can you help me in giving me some idea to deal with this?
>> bcsb09s-imac52:bin bcsb09$ pdb2gmx -f 1aml.pdb -p 1aml.top -o 1aml.gro
> <snip>
>> -------------------------------------------------------
>> Program pdb2gmx, VERSION 3.3.3
>> Source code file: futil.c, line: 313
>> File input/output error:
>> 1aml.top
>> -------------------------------------------------------
> This means it can't write 1aml.top, which likely means you don't have write
> permission to the directory in which pdb2gmx resides. This is a Good Thing.
> You should do daily work in a suitable subdirectory of (say) your home
> directory, and adjust your environment variables to give you ready access to
> GROMACS stuff by using "source /path/to/GMXRC" using the  path in which you
> installed the GROMACS binaries. I guess this is your attempted working
> directory above.
>  I seem to be having problem in running the test tun as well. Below is its
>> output:
>> bcsb09s-imac52:bin bcsb09$ ./gmxtest.pl
>> Usage: ./gmxtest.pl [ -np N ] [-verbose ] [ -double ] [ simple | complex |
>> kernel | pdb2gmx | all ]
>>   or: ./gmxtest.pl clean | refclean | dist
> Again this won't work in a directory in which you don't have write
> permissions. The above message tells you that an empty command line isn't
> acceptable to gmxtest.pl. *Technically* it ought to be acceptable per the
> usage line, since square brackets denote optional things and |-symbols
> denote a series of mutually-exclusive possibilities. I think the brackets
> should be missing around "simple | complex | kernel | pdb2gmx | all".
> Mark
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