Hi, Scott.
Now, I got what you problem is. By default DALTON expects coordinates in
Bohrs, not in Angstroms.
So you should multiply each end every cartesian coordinate
by bohrsToAngstroms = 0.52917720859.
Regards,
Anton
On Tue, Oct 8, 2013 at 11:17 PM, Anton Simakov <kemii...@gmail.com> wrote:
> 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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