[gmx-users] cannot generate .top file

[Mark Abraham]

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