On 4/30/12 12:29 PM, Lara Bunte wrote:
Hi Justin
I got the error
Can not open file:
topol.tpr
if I type trjconv -n index.ndx -f molecule.pdb -o output.pdb -s
and I got the error
Can not open file:
traj.xtc
if I type trjconv -n index.ndx -f -s molecule.pdb -o output.pdb
What is the problem?
Again, as has been stated several times, giving any Gromacs program a command
line option (like -s or -f) in the absence of an explicit file name, will cause
the program to look for a default file name (which are listed in the manual or
with -h). In the first case, with no file name given to -s, trjconv looks for
topol.tpr and fails. In the second case, -f is looking for traj.xtc and fails.
Provide explicit file names for all options, unless you actually have used the
default names (which in your case, you haven't).
Please go back to my previous advice: "Supply your .pdb file to the -s flag."
That doesn't mean add -s to the command line and expect magic to happen ;) It
means you need to invoke the -s flag to signal that you are providing a file
there, and then name that file. For pedantic purposes:
trjconv -n index.ndx -f molecule.pdb -s molecule.pdb -o output.pdb
The -f flag specifies the file that is being operated on.
The -s flag specifies a file from which (in this case) atom and residue names
are being read. It is necessary because your output format (.pdb) requires this
information.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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