On Tue, Apr 12, 2011 at 12:12 PM, Yao-Chi Chen <backy2010.chen.gmail.com>wrote:
> Hi, all:
>
> For a given protein chain with 208 residues, I used the mm_pbsa.pl to run
> a
> energy decomposition by residue.
> Conditions with two different salt concentrations were tried, which is
> SALTCON respectively set as 0 and 10.
>
SALTCON is the salt concentration in M. 10 is a bit extreme (indeed, the
approximation used isn't really valid past 0.1). Consult the literature on
this (Amber manual has references).
The salt concentration is a debye screening parameter. The formula can be
found in one of those papers, and it's also in the Amber manual in the very
beginning of chapter 3. I would suggest consulting the manual, as it is
generally a good place to start. It outlines the basic theory and provides
references for more in-depth analysis.
> But the calculation results are slightly different and the difference was
> only reflected in the EGB term. ( the electrostatic term was no changed at
> all). Could anyone explain this to me? In the last, the input
>
Again, look at the formulas. It's only supposed to affect EGB.
> parameter/structure files that I fed to MMPBSA were listed. Meanwhile, I
> extracted the energy decomposition from residue Arg.
>
> The data in the in the 4th and 6th columns are the ELE and EGB term based
> on SALTCON=0,
> The data in the 9th and 11th columns are the ELE and EGB term based on
> SALTCON=10.
>
The columns are garbled. I couldn't tell what was what. Also note that the
decomposition analysis is an approximation. GB is not strictly pairwise
decomposable (see previous posts that discuss this), since the effective
radii depend on the everybody (within rgbmax).
The results you're getting seem reasonable, and I would suggest consulting
the literature for discussions there.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Apr 12 2011 - 12:30:05 PDT
