VMD-L Mailing List

From: Jan Saam (jan.saam_at_charite.de)
Date: Thu Feb 22 2007 - 18:43:57 CST

Hi Javaria,

the .chk file is a checkpoint file for Gaussian from which you can restart
a simulation or from which you can retrieve selected data for your next
simulation. However, Gaussian does not append to this binary file, it
overwrites it.

Paratool uses the .chk file to get the coordinates and wave function from
your Geometry optimization in order to save computation time. Since we
want to keep the .chk from the optimization Paratool copies the file to a
new name (e.g. *_opt.chk -> *_sp.chk).

Your problem ist most likely not due to the checkpoint files, because this
file is inyour case only copied under Windows but not edited. It is
written by Gaussian under Unix and also used by Gaussian only.

I guess the problem is with the .com file. Windows and Unix use different
newline characters. You can see this when you open a Windos edited file in
an editor under unix. You'll most likely see sommething like ^M at the end
of each line.

Here are a few sed scripts that convert text files between the Unix and
Windows format (they stem from a very useful collection of sed examples
found here: http://sed.sourceforge.net/sed1line.txt).

 # IN UNIX ENVIRONMENT: convert DOS newlines (CR/LF) to Unix format
 sed 's/.$//' # assumes that all lines end with CR/LF

 # IN UNIX ENVIRONMENT: convert Unix newlines (LF) to DOS format
 sed "s/$/`echo -e \\\r`/" # command line under ksh
 sed 's/$'"/`echo \\\r`/" # command line under bash
 sed "s/$/`echo \\\r`/" # command line under zsh
 sed 's/$/\r/' # gsed 3.02.80

 # IN DOS ENVIRONMENT: convert Unix newlines (LF) to DOS format
 sed "s/$//" # method 1
 sed -n p # method 2

 # IN DOS ENVIRONMENT: convert DOS newlines (CR/LF) to Unix format
 # Can only be done with UnxUtils sed, version 4.0.7 or higher.
 # Cannot be done with other DOS versions of sed. Use "tr" instead.
 sed "s/\r//" infile >outfile # UnxUtils sed v4.0.7 or higher
 tr -d \r <infile >outfile # GNU tr version 1.22 or higher

Good luck,
Jan

> Hi
>
> It is regarding paratool option for setting up QM singly point
> calculation.
>
> (I am using paratool on windows system and using gaussian on a unix system
> at remote location)
>
> When I set up an single point calculation from paratool, it requires me to
> provide .chk file (which i suppose is from the geometry optimization of
> same base molecule) (I have that .chk file on unix environment)
> When I provide the .chk file to paratool and generate a .com file , it
> generates a new .chk file. (that is on my windows system)
>
> My question is which chk file is then used during gaussian single point
> calculation. Or both of them need to be there in the working directory (at
> unix system) for the gaussian calculation? and what is their format? does
> .chk file need conversion for use on windows (when generated on unix and
> transfered to windows) and for use on unix (when genertaed by paratool on
> windows)?
>
> I am asking this question because I a getting an error while executing
> single point calculation on gaussian which is;
> Error termination in NtrErr:
> NtrErr Called from FileIO.
>
> I am suspecting it is because guassian is unable to read a file.
>
> Regards,
> Javaria
>