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:[email protected]
------------------------------------------------------------------------
没有广告的终身免费邮箱,www.yeah.net <http://www.yeah.net/?from=footer>
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
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
[email protected] [email protected] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
