Dear AMBER-Community,
I would like to add extra points of charge to molecules that contain
halogens to simulate sigma holes, but I am having trouble understanding
how to actually determine the postition of these extra points and
placing them in the topology file. I looked at the tutorials available
on the AMBER homepage and read everything available about that topic in
the mailing list archive, but I just don't get it.
I perfomed the gaussian optimization of the molecules in question,
calculated the RESP charges and so on. But how can I determine the
coordinates for the extra points? How do I know what charge it should
have? Could someone maybe provide me with a kind of 'explanation for
dummies'. I feel like, I am missing just one simple sentence, one
keyword, or anything like that, that could suddenly make me understand
what I have to do. I am just so lost.
Thanks for your help.
Friederike Leßmöllmann
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Received on Mon Aug 28 2023 - 12:30:02 PDT
