Hi Tang, read carefully: http://www.pdb.org/robohelp_f/#site_navigation/general_faq.htm
and get yourself prepared in how a pdb file is set up. If you want to do simulations, get started with knowing the basics first. Cheers Steffen > Dear all, > I have got a pdb file by command g_rmsf and option -oq, and the content > of the file is like this: > TITLE Protein in water > REMARK THIS IS A SIMULATION BOX > CRYST1 148.918 148.918 148.428 59.89 59.89 90.00 P 1 1 > MODEL 1 > ATOM 47354 CA ALA I9967 60.915 88.765 42.075 1.00 92.09 > ATOM 47364 CA GLY I9968 60.037 91.017 39.099 1.00 31.09 > ATOM 47371 CA PHE I9969 59.892 94.727 38.149 1.00 13.34 > ATOM 47391 CA LYS I9970 56.778 96.973 38.146 1.00 13.59 > ATOM 47413 CA ALA I9971 57.412 100.730 38.292 1.00 8.88 > ATOM 47423 CA GLY I9972 55.243 102.910 40.429 1.00 8.42 > ATOM 47430 CA VAL I9973 55.349 104.629 43.777 1.00 6.96 > ATOM 47446 CA LYS I9974 55.039 102.584 47.023 1.00 10.56 > ATOM 47468 CA ASP I9975 53.919 102.844 50.642 1.00 8.59 > ATOM 47480 CA TYR I9976 56.618 101.675 53.096 1.00 5.41 > ATOM 47501 CA ARG I9977 54.179 100.074 55.607 1.00 6.66 > ATOM 47525 CA LEU I9978 53.642 97.083 53.329 1.00 10.59 > ATOM 47544 CA THR I9979 57.043 95.266 53.147 1.00 10.24 > ATOM 47558 CA TYR I9980 59.307 96.919 55.730 1.00 4.74 > ATOM 47579 CA TYR I9981 57.141 96.770 58.853 1.00 4.52 > ATOM 47600 CA THR I9982 57.423 93.001 59.524 1.00 5.61 > ATOM 47613 CA PRO I9983 55.634 91.722 62.707 1.00 11.23 > ATOM 47628 CA ASP I9984 56.655 88.019 62.809 1.00 13.38 > ATOM 47640 CA TYR I9985 60.439 88.728 62.349 1.00 9.58 > Could you tell me which column should be the b-factor? B-factor is the > thermal deviation of the atom, and could you tell me how the gromacs > gives the values of b-factor for each atom in detail? > > Thank you! > > > Tang Jiaowei > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.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 > -- Dipl.-Chem. Steffen Wolf Fellow of the Ruhr-University Research School Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: [EMAIL PROTECTED] Web: http://www.bph.rub.de _______________________________________________ gmx-users mailing list [email protected] http://www.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
