questions on t2x

[zhangustc]

one question on t2x:
When I finished the optimization and start to run t2x, system always gave the following information:

[lab@ h2o.structure]$ t2x > h2o.fianl1.xyz
tail: cannot open `+2' for reading: No such file or directory
tail: cannot open `+2' for reading: No such file or directory


How can I solve this problem?

Another question:Is there any program can cover the atomic unit output to angstrom output?
Thanks a lot!

[antti_karttunen]

Hello,

What operating system/distribution are you running? I have noticed that at least in Fedora Core 5 /usr/bin/tail cannot understand the "tail +2" notation used in t2x. If this is your case, I suggest you to replace /usr/bin/tail with a properly working binary. Another way would be to edit the t2x script by replacing the "tail +2" with "sed 1d" or something like that. The Fedora distribution has had some other problems similar to this, too. If you want to use a Redhat-like distribution, I can recommend CentOS. It is based on RHEL and has worked very well for us.

[scope]

My advise is to generally use OpenBabel.
You can get it here: openbabel.sourceforge.net

The Syntax is very easy and it knows practically any quantum chemistry format, even the exotic ones. The t2x script always has given me problems (in many cases: A missing blank line before the coordinate definition-which results in 1 atom missing if you use gOpenmol for example).
To convert from Turbomole to XYZ, just run
"babel -itmol coord -oxyz coord.xyz" (if your coordinate file is named "coord").

HTH
Nils

[christof.haettig]

t2x definitely works (has worked for many years) correctly, provided the unix/linux commands called by it work as they should!

Sorry Nils, but the problems you write about are NOT the fault of the t2x command. Is it possible that you selected the wrong xyz format in
the gopenmol program? In previous versions of gopenmol one had to select between different xyz/xmol formats, the
t2x script writes an xyz file with two header lines (first line: number of atoms, second line: energy) as they are recognized
by many viewers (e.g. jmol, molekel). Gopenmol knows this format as 'xmol', while the 'xyz' format is in gopenmol defined 
with only one header line.

This problems does not  occur with gopenmol 3.00, which determines the file format automatically.

Best regards,
           Christof

[scope]

Thanks Christof for pointing this out. I rechecked and in gopenmol 3.0 it really works :-)

[martijn]

Hi,

I had a similar problem on Ubuntu (8.04) and seemed to have succesfullly resolved it by hacking the t2x script and simply replacing all the "tail +x" with "tail -n +x". 

Cheers,

Martijn