AMBER Archive (2008)

Subject: Re: AMBER: BCC charges

From: Thomas Exner (thomas.exner_at_uni-konstanz.de)
Date: Wed Jan 23 2008 - 04:11:36 CST


Dear Ross,

thank you very much for your help. The problem was the optimization. I
checked the parameters in divcon and g03 for H, C, N, and S and they are
exactly the same. But I did only a single point calculation in gaussian.
Also deactivating the optimization in divcon resulted in exactly the
same charges. Using optimization in both programs leads to slightly
different charges but also different geometries. Unfortunatelly, this is
not directly apparent from the output, because antechamber uses the
input geometry and not the optimized one in the output.

Thomas

Ross Walker schrieb:
> Dear Thomas,
>
>> due to the larger flexibility of the gaussian input format, I
>> would like
>> to substitute the divcon program by g03 for the calculation
>> of AM1-BCC
>> charges used as GAFF parameters of small molecules. In
>> prinziple, this
>> works pretty well after some modifications of the antechamber
>> program.
>> But the AM1-BCC charges are much different to the original
>> results using
>> divcon. Here are the results for ethanol as an example:
>
> As a first guess this may be due the fact that Gaussian uses different
> values for a number of constants. Take a look at the supplemental material
> of the following paper:
>
> http://www3.interscience.wiley.com/cgi-bin/abstract/117859892/ABSTRACT
>
> Try incorporating the changes described there into G03, recompile it and
> then run it again and see if the resulting charges change by an appropriate
> amount. They won't come out the same as Divcon since that uses yet another
> set of values for the constants so you'd have to make the equivalent changes
> in Divcon as well. However, you should be able to gauge how much of an
> effect small changes in the values of the constants have on the predicted
> charges and so determine if this may indeed be the cause or there is
> something else going on.
>
> I note that the two outputs you showed had identical coordinates in both
> Divcon and G03. Did you optimize them independently in both to get this? If
> you did I find that amazing. However, I assume more likely what you did is
> minimize in one and then copy the coordinates over to the other yes? If this
> is the case you may want to take that set of "truncated" coordinate (since
> they are only to 4 decimal places) and run it through both divcon and
> gaussian as a single point calculation to see how much that changes the
> charges. It is possible that part of what you see comes from the truncation,
> I.e. it was truncated in g03 but Divcon internally was using the full
> precision. Again, just a guess.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
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-- 
________________________________________________________________________________

Dr. Thomas E. Exner Juniorprofessur "Theoretische Chemische Dynamik" Fachbereich Chemie Universitšt Konstanz 78457 Konstanz

Tel.: +49-(0)7531-882015 Fax: +49-(0)7531-883587 Email: thomas.exner_at_uni-konstanz.de ________________________________________________________________________________ ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu