[DFTB-Plus-User] N-H skf files

Lin Song qxsxmu2010 at gmail.com
Fri Mar 24 18:12:51 CET 2017

Hi Dr. Bálint Aradi,

Thank you very much for your reply and kind suggestions. I get what you’re saying. But since it is implemented in AMBER, I’d have to check if we can do this mix-atom-type thing. Probably not since I don’t see any keywords for that. I might need to contact the author of the modified parameters, but I appreciate your help!


> On Mar 21, 2017, at 9:50 AM, Bálint Aradi <aradi at uni-bremen.de> wrote:
> Dear Lin,
>> I’m confused which N-H skf file should I use, the mio-1-1 set or the 
>> miomod:nh set? My system is an enzyme and I’m using DFTB as the
>> quantum method to do QM/MM MD studies in AMBER. Under the miomod:nh
>> page, I found that it is modified to reproduce the sp3 nitrogen and
>> proton affinity better, but the spa nitrogen are descibed correctly
>> by the original mio-1-1 set. Now my system has both sp2 and sp3
>> nitrogen, should I use the original mio-1-1 set or the modified
>> miomod:nh set? I appreciate any help!
> I am not really an expert on those systems and never used those
> 'improved' modified interactions, so be critical about any advice I give
> below. Probably, you should try to contact the SK-file authors directly...
> But anyway, I guess, you have two options. You could use the original
> mio-1-1 for all elements and check results on small relevant systems
> against ab initio. If it is not satisfying at all, you could introduce
> two type of nitrogens in your system, one for the sp2 and one for the
> sp3 configuration and use the different Sk-files for them. On the
> SK-file level, that is somewhat messy, you would have create all
> interacations of the second N type (let's call it N2) with all other
> elements (including the original N). For most interaction, you just copy
> and rename the original interactions, while for N-H and H-N you would
> take it from the modified set.
> Best regards,
> Bálint
> -- 
> Dr. Bálint Aradi
> Bremen Center for Computational Materials Science, University of Bremen
> http://www.bccms.uni-bremen.de/cms/people/b-aradi/
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