Hello,
I have question about calculating binding energy using
MM_PBSA module in AMBER.
I never added any solvent cap while creating topology
file --> Can i still use PB to calculate binding
energy.
I used periodic boundary conditions for MD --> whihc
turns off Generalized Born --> can I still calculate
binding energy using PB=1 in MM_PBSA.
Do I have any other options to calculate binding
energy.
my equilibiration.in file looks like this:
Molecular dynamics Run
&cntrl
imin=0, ntx=5, irest=1, ntb=2,
ntpr=500, ntwx=500, ntf=1, cut=15.0, ntp=1,
nstlim=100000, dt=0.001,
ntt=1, tempi=300.0, temp0=300.0,
/
And now I want to calculate binding energy. Which
methid I use use PB or GB?? can some one suggest
something in this regrad?
Thanks,
Varsha
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Received on Sun Nov 19 2006 - 06:07:17 PST
