different molecules in an input file

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olicar
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Joined: 21 Jul 2016, 11:39
First name(s): Oliver
Last name(s): Carrillo
Affiliation: Scuola Normale Superiore di Pisa
Country: Italy

different molecules in an input file

Post by olicar » 21 Jul 2016, 13:41

Hi all,
I'm trying to run dalton for a solution made of one molecule of tyrosine surrounded by molecules of water but I'm doing something wrong because I get this error:

INPUT ERROR: Number of symmetry independent centers invalid

I suppose it's related to the .mol file. I wrote it with all the atoms of the system with no specification of the molecule they belong, can that be the error? How can
I fix it? I send you my input file wattyr.mol

Thank you very much!
Oliver
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kennethruud
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Affiliation: UiT The Arctic University of Norway
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Re: different molecules in an input file

Post by kennethruud » 21 Jul 2016, 14:34

Dear Oliver,

In general it would be useful to have the output file in order to more clearly see what the error results in (and it contains the input files you use).

I thus cannot necessarily tell what the exact cause of the error you see. However, I see you want to include 4000 water molecules in the ab initio calculation with an aug-cc-pVDZ basis set which will give you around 16000 basis functions. There is no way this is going to work with Dalton (and you will wait forever it the calculation ever starts).

Please consider using a polarizable embedding strategy, possibly with a few water molecules included in the nearest solvent shell. Alternatively, continuum model with a supermolecular approach may also give good results.


Best regards,

Kenneth

hjaaj
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First name(s): Hans Jørgen
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Re: different molecules in an input file

Post by hjaaj » 30 Jul 2016, 23:00

Kenneth is right with respect to your calculation being too big for Dalton.

However, the error message came because you forgot to specify "Atoms=" in front of the number of atoms for each atom type. For example, the following line from your .mol file:

Code: Select all

     Charge=8.     3916
should have been:

Code: Select all

     Charge=8.    Atoms=3916
-- Hans Jørgen.

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