The issue was the permissions, thanks or your input!
On Sat, Nov 17, 2012 at 4:42 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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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>
--
Maxier Acosta Santiago
Undergraduate Student
JMR LAB
Department of Chemistry
University of Puerto Rico,
Rio Piedras Campus
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Received on Sun Nov 18 2012 - 08:30:02 PST
