From: Eifler, Jay Q. (UMKC-Student) (
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

this question.

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