Hi, Scott.
I don't have a solution, but just for your information.
Extension *.mol is very common and the fact is that this is not strangely
formatted mol (MDL MOL) file, but rather quite valid molecule input file
for DALTON.
I'm not sure can Open Babel read DALTON mol files or not, but it seems like
it can not. So first you need to convert to something else, say to xyz file.
Regards, Anton
On Tue, Oct 8, 2013 at 8:36 PM, scott_m <js...@cam.ac.uk> wrote:
> Hi all,
>
> I am trying to extract the structure from the following strangely formatted
> mol file:
>
> BASIS
> cc-pVTZ
> PP
> EXCITATION DIAGNOSTIC
> Atomtypes=3 Nosymmetry
> Charge=6.0 Atoms=10
> C 2.2706222585 4.7730173284 0.0000000000
> C -2.2706222585 4.7730173284 0.0000000000
> C 0.0000000000 6.1111121474 0.0000000000
> C 2.2816826330 2.1387165841 0.0000000000
> C -2.2816826330 2.1387165841 0.0000000000
> C 0.0000000000 0.7923464742 0.0000000000
> C 2.1197819099 -3.4258994126 0.0000000000
> C -2.1197819099 -3.4258994126 0.0000000000
> C 1.3395610232 -5.9107336961 0.0000000000
> C -1.3395610232 -5.9107336961 0.0000000000
> Charge=7.0 Atoms=1
> N 0.0000000000 -1.8918071168 0.0000000000
> Charge=1.0 Atoms=9
> H 4.0627785591 5.7776147665 0.0000000000
> H -4.0627785591 5.7776147665 0.0000000000
> H 0.0000000000 8.1643586785 0.0000000000
> H 4.0806204132 1.1593701311 0.0000000000
> H -4.0806204132 1.1593701311 0.0000000000
> H 4.0065792553 -2.6563688490 0.0000000000
> H -4.0065792553 -2.6563688490 0.0000000000
> H 2.5755781273 -7.5400732042 0.0000000000
> H -2.5755781273 -7.5400732042 0.0000000000
>
>
> I've tried just using the coordinates but I get an error for setting up the
> forcefield. The coordinates are taken from MP2 calculations but when I view
> the structure in avogadro the interatomic distances are all too long. It
> looks like they need to be scaled. Any advise here?
>
> All the best,
>
> Scott
>
>
>
>
> --
> View this message in context:
> http://forums.openbabel.org/Unable-to-set-up-forcefield-for-coordinates-from-mol-file-tp4656682.html
> Sent from the General discussion mailing list archive at Nabble.com.
>
>
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