David van der Spoel spoel at xray.bmc.uu.se
Wed Aug 19 19:18:56 CEST 2009

dxli75 wrote:
> Dear All,
>
>
>
>     I have make a free energy landscape by using the data of RMSD and
> H-bond number of main chain of a protein according to the
> following method. I am not sure if the method does work. If not, Could
> you give me some advises? Thank you!
>
> PS: Method
>
>    1. Obtained the RMSD and the number of H-bond of mainchain of the
> protein by using g_rms and g_hbond commonds;

Then you can try using g_sham as well.

>
>    2. Copy above two groups of values (RMSD and H-bond number) into
> Origin Software. first column is values of H-bond number, second column
> is RMSD;
>
> 3. Statistics > Descriptive Statistics > 2D Frequency Count in Origin,
> and obtained a matrix named as"TwoD FreqCounts";
>
> 4. Convert the above matrix into worksheet with type of xyz, and  got
> the values in the third column (frequency counts of RMSD and H-bond number);
>
> 5. Calculate the frequency count into normalized possibility;
>
> 6. Select the maximal or minimal possibility as control value.
>
>    If  you select the maximal possibility (Pmax) as control value, the
> ΔG = G_x - G_max = -k_B Tln(Px/Pmax) > 0;
>
>    If  you select the minimal possibility (Pmin) as control value, the
> ΔG = G_x - G_min = -k_B Tln(Px/Pmin) < 0;
>
> Calculate all the values of (Px/Pmax) or (Px/Pmin) as the new third
> column. Here I choose Pmin (frequency count = 1) as control value, and
> get negative values of free energies;
>
> 7. Convert the values in above three columns into a new matrix by using
> the method of XYZ Gridding.
>
> 8. According to the above new matrix, plot the final free energy
> landscape.
>
>
>
>
> --
> Dx Li
> ---------------------------------------
> Mechanic Engineering Department
> College of Engineering and Computing
> University of South Carolina
> 300, Main Street, 29208
> Columbia, SC
> Tel: 803-9316307(M); 803-7771299(O)
> E-mail:Daixi at cec.sc.edu
>
>
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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