up :) It's appeared two additional questions. 1) In addition to the pca's cross-correlation maps I wounder to know about possibility of calculation of such cross-correlation's from the trajectories indirectly without calculation of the covariance matrices.
2) is there any way to calculate degree of fluctuations of side-chains ( degree of torsion's dynamics) from the different trajectories and to compare it ? E.g I have one protein in two different (apo and holo) forms. I've calculated two trajectories for both structures and observed different degree of dynamics in case of each structure ( e.g fluctuations in case of apo form were more frequent than in case of liganded form). IS there any way to direct mesure and comprison of such side-chain's dynamics for two trajectories? James 2012/8/15, James Starlight <jmsstarli...@gmail.com>: > Dear Gromacs users! > > > I want to obtain Cross-correlation maps ( for indication of the > cross-correlated fluctuations of the residues). > The example of such maps can be found here > http://pubs.acs.org/doi/abs/10.1021/ja076046a > > I found that modificied version of the G_covar from users > contributions can do such things. But because of the older version of > that program (3.3.3) I've obtained the below error using it with 4.5.5 > gromacs > > > Reading file md_GO.tpr, VERSION 4.5.5 (single precision) > > ------------------------------------------------------- > Program g_covar_mod, VERSION 3.3.3 > Source code file: tpxio.c, line: 1192 > > Fatal error: > reading tpx file (md_GO.tpr) version 73 with version 40 program > ------------------------------------------------------- > > > Is there newest versions of the G_covar for such things or > alternativelly any others ways to calculate such correlations maps ? > > Thanks for help > > James > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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