AMBER Archive (2006)

Subject: AMBER: MM_PBSA

From: Varsha Goyal (vgusp_at_yahoo.ca)
Date: Wed Nov 15 2006 - 20:27:15 CST

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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