From: AHMET BAKAN (ABAKAN_at_KU.EDU.TR)
Date: Sat Apr 24 2004 - 21:09:45 CDT
I am making some binding simulations. To get an idea of binding energy (BE) I simply perform the calculation E(binding) = E(complex) ? [E(protein) + E(inhibitor)].
What I want to calculate is the energy of hyrdoren bondings between two chains either as simulation takes place or when analyzing trajectory file.
What I found to make use of is Pair Interaction Calculations. I give the list of possible h-bonding atom pairs and get forces. My questions are:
- Is there a way to update the list, since after long simulation some pairs are lost and new pairs are formed.
- I get total force on atoms, how should I change this to energy?
- Is the total attraction force between two chains within the cutoff distance a reliable measure of binding?
Also, I want to ask some more general questions:
- Is there a better measure of BE or method for calculating BE with NAMD.
- Will it be possible to make an extensive use of TCL commands like atomselect within NAMD?
Thanks in advance for any kind of advice,
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