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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