On Sat, Nov 17, 2012 at 3:06 PM, Maxier Acosta Santiago <
maxier.acosta.upr.edu> wrote:
> Greetings:
> I am trying to run
>
> *parmchk –i RED_OUTPUT.mol2 -f mol2 -o frcmod*
>
> but the response i am getting is:
>
> *Cannot open file to read in rmol2(), exit*
>
This suggests that RED_OUTPUT.mol2 does not exist. Is this true? If it
does exist, do you have read permissions for it? You can test the
permissions by simply opening that file in a text editor.
Another possibility is that you're not inputting the command correctly. I
can't tell for certain from the email, but the dash in front of the i
appears to be a non-ascii n- or m-dash, rather than a normal hyphen.
If you are certain that RED_OUTPUT.mol2 exists in the current directory,
this error may be caused by improperly copying-and-pasting the command from
a source that automatically converted the dash to an n- or m-dash, or it
may be caused by your mail client automatically turning two dashes into an
m-dash or n-dash.
If it is the first case, try typing the command into the terminal (do not
copy-and-paste), making sure that the option flags are preceeded by a
normal hyphen and not another type of dash.
If it is the second case, take out the second dash in front of the -i flag
(it only recognizes 1 as far as I know).
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Nov 17 2012 - 13:00:02 PST
