Hi Tsjerk,
I have been thinking about this way, but I do not think have parameters
for C(-dum)-C to C-C-C, for example, the distance between the 1st and
3rd carbons.
thanks
Qiang
Tsjerk Wassenaar wrote:
Hi Qiang,
Couldn't you do it by shortening the chain, turning on/off one of the
CH2 groups? You only have to mind perturbing the bonding and such in
the right way then.
Cheers,
Tsjerk
On Sat, Sep 27, 2008 at 6:32 PM, 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
Mobley's suggetion, 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?
thanks a lot
Qiang
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