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
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
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
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
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
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
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