Hi David,
Thanks for clarification.
Yes, you are right. I am morphing only parts of the sidechain.
Qiang
David Mobley wrote:
Hi,
As long as you end up with the same charge in the initial and final
states, you should be OK. It's only if your total transformation
involves a change of net charge that you need to worry. So you should
be fine if you turn off the charges on D, change the LJ interactions,
and turn back on the charges on E.
If I were you, I probably would not turn off the charges entirely --
after all, D and E share many atoms. I would only turn off charges on
the atoms that you are going to modify.
David
On Fri, Sep 26, 2008 at 2:14 AM, friendli <[EMAIL PROTECTED]> wrote:
Dear all,
I have a mutation free energy calculation from D(asp) to E(glu). The charge
is not changed for the overall mutation. However, following Dr. David
Molbey's suggesion, electrostatic and VDW interaction should be modified
separately, so in the first step we need to turn off the charge from D(-1)
to D(0).
I learn from the mailing list that it is problematic to do FE calculations
with different charges for initial and final states.
So is that safe to turn off the charge for D and turn on the same charge for
E in this case?
If not, it that OK to perform mutation FE calculation in one step?
or there is no safe way to handle this kind mutations, i.e. mutating charge
groups, currently without special correction?
thank a lot
Qiang
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