Hi, After searching though gmxuserlist I found the relevant thread for ED... I followed the following steps :- 1) g_covar - to generate a covariance matrix and diagonalize it (for c-alpha atoms only) 2) g_anaeig - to generate eigen vectors 3)g_rmsf - for calculating RMSD of first 8 eigen vectors , I got an error at this step that -
Fatal error: Molecule in topology has atom numbers below and above natoms (230). You are probably trying to use a trajectory which does not match the first 230 a toms of the run input file. You can make a matching run input file with tpbconv. ------------------------------------------------------- "California, R.I.P." (Red Hot Chili Peppars) 4) then I used make_ndx - for generating an index file containing only c-alpha atoms..which was done successfully 5) Further I used tpbconv - to generate a .tpr file for calculating the rmsf ... but I am getting the following error at this step .. Fatal error: Molecule in topology has atom numbers below and above natoms (230). You are probably trying to use a trajectory which does not match the first 230 a toms of the run input file. You can make a matching run input file with tpbconv. ------------------------------------------------------- "California, R.I.P." (Red Hot Chili Peppars) Pls help what has to be done in order to generate the .tpr file ... -- 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
-- 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
