Re: pKa calculation with thermodynamic integration (TI)

From: Hannes Loeffler (
Date: Wed May 17 2017 - 03:37:52 CDT

> Is that what I am supposed to do? if so, how can I tight (for
> example) CD and CD1 atoms together by a harmonic restraint? at the
> beginning, there is no distance between them.

You need to mark the outgoing group with -1 in the column that you have
chosen (alchCol). Look into the extraBonds feature to set additional


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