Dear Dr. Case,
Thanks a lot for your prompt reply!
When there is no explicit counterions in my GB simulations (IGB=2), I use MM-GBSA for calculating some energies. GB parameters are as following (Amber 7):
IGB=2
SALTCON=0.00;
EXTDIEL=80.0;
SURFTEN=0.0072;
SURFOFF=0.00;
1ns GB simulations was done for a protein-protein complex, and 100 or 10 snapshots was extracted during equilibrated state shown by little change of RMSD. When using MM-GBSA, I got relative binding free energy (excluding entropy contribution) is about -300 kcal/mol, which seems 1-2 orders of magnitude greater than would be physically reasonable. After changing "SALTCON=0.00" into "SALTCON=0.10", there is little change for relative binding free energy.
Here, there is something wrong with my used GB parameters? Otherwise, how to explain my results?
Looking forward to your help once more, and thank you very much once more!
My best to you!
Wu Yingliang
======= 2005-04-21 08:22:00 Cotents：=======
>On Thu, Apr 21, 2005, Wu Yingliang wrote:
>
>> It is essential to neutralize system in GB simulations?
>
>My general recommendation is to avoid adding explicit counterions in GB
>simulations. The distribution of "salt" in the solution can be approximated
>at a Debye-Huckel-like level (see the saltcon variable).
>
>.....dac
>
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Received on Fri Apr 22 2005 - 03:53:00 PDT
