I searched the user list in order to get some idea about calculating cosine content of first PCA .. but I am not able to do so ??
Can u direct me to a good thread or discussion.. On Tue, Feb 1, 2011 at 2:04 AM, bharat gupta <bharat.85.m...@gmail.com>wrote: > Thanks for the reply ... > > I am following this thread - > http://oldwww.gromacs.org/pipermail/gmx-users/2004-May/010438.html > <http://oldwww.gromacs.org/pipermail/gmx-users/2004-May/010438.html>Also > I read the following paper http://pubs.acs.org/doi/abs/10.1021/jp983120q > (Internal > dynamics of GFP) in which they have carried out such projections of the > eigen vector in order to find the regions showing minimum and maximum > amplitudes.. > > What I am thinking is shall I take those c-alpha atoms that are well stable > and equilibrated after referring to RMSD graph generated after simulation > ... > > I am stating here what I have done so far and what I have to analyze :- > > I exchanged the loops regions of GFP with loops of longer length taken from > pdb .. I simulated both the crystal str. and modeled strs. to compare how > the loop incorporation leads to the change in the structure of GFP .... > Since the RMSD of the GFP crystal str and that of model are in comparable > range .. I thought of looking at the motions of loops in the structure that > are giving such fluctuations in RMSD of model and for that I decided to > generate eigen vectors and project them in 3d (like the one given in paper > mentioned above) to see how that particular loop behaves .. I don't know > whether what I have hypothesized is correct or not .. since I am not able to > find any other insilico method apart from MDS for such a study .. Also if my > prediction comes out to be good enough I have to carry out such insertion in > the wet lab and has to check for fluorescence ..any help in this regard will > be appreciated... > > > On Tue, Feb 1, 2011 at 1:28 AM, Tsjerk Wassenaar <tsje...@gmail.com>wrote: > >> Hi Bharat, >> >> On Tue, Feb 1, 2011 at 8:33 AM, bharat gupta <bharat.85.m...@gmail.com> >> wrote: >> > Hi, >> > After searching though gmxuserlist I found the relevant thread for ED... >> I >> > followed the following steps :- >> >> What thread are you referring to? >> >> > 1) g_covar - to generate a covariance matrix and diagonalize it (for >> c-alpha >> > atoms only) >> > 2) g_anaeig - to generate eigen vectors >> >> g_covar calculates the eigenvectors. It's what you end up with through >> diagonalization. >> >> > 3)g_rmsf - for calculating RMSD of first 8 eigen vectors , I got an >> error at >> > this step that - >> >> g_rmsf is not for calculating RMSD, and hasn't got much to do with >> eigenvector analysis. That's what g_anaeig is for (like with the >> option -rmsf). Using g_anaeig will avoid the error you observe. >> >> As a side note, 3 ns is rather short for this sort of thing. You have >> to check the cosine content of the first principal components to see >> if you've reached equilibrium already. >> >> Cheers, >> >> Tsjerk >> >> >> >> -- >> Tsjerk A. Wassenaar, Ph.D. >> >> post-doctoral researcher >> Molecular Dynamics Group >> * Groningen Institute for Biomolecular Research and Biotechnology >> * Zernike Institute for Advanced Materials >> University of Groningen >> The Netherlands >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > Bharat > Ph.D. Candidate > Room No. : 7202A, 2nd Floor > Biomolecular Engineering Laboratory > Division of Chemical Engineering and Polymer Science > Pusan National University > Busan -609735 > South Korea > Lab phone no. - +82-51-510-3680, +82-51-583-8343 > Mobile no. - 010-5818-3680 > E-mail : monu46...@yahoo.com > > -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com
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