From: Eifler, Jay Q. (UMKC-Student) (jqewt2_at_mail.umkc.edu)
Date: Mon Mar 31 2014 - 11:47:16 CDT
I've gone through the first VMD and NAMD tutorials and have read
around in various articles but still am puzzled with this question:
I'm doing quantum mechanical calculations with our own local software
and have partial charge results on a whole protein. It seems MD software
only uses partial charges from model peptides, etc. and not the result from
the full moelcule, so my question is:
How do I use these partial charges in NAMD rather than the partial charges
that are begun with from model compounds?
I understand there's a lot of parameterization to emprical values but I have
an ab-initio result. I also could produce the electronic potential and have a
wave function as well.
Really I want to be able to link our results into MD simulations (of course)
like NAMD or perhaps Amber which uses the RESP method.
Maybe I need to do more homework but everyone seems to avoid addressing
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