On Wed, 2010-06-30 at 13:07 +0200, Erik Marklund wrote: > leila karami skrev: > > Hi all > > > > pdb file for my protein was obtained by solution NMR. this file is as > > follows : > > > > ATOM 1 N GLY A 1 -25.349 -8.577 4.055 1.00 0.00 > > ATOM 2 CA GLY A 1 -24.037 -8.099 4.448 1.00 0.00 > > ATOM 3 C GLY A 1 -23.580 -6.913 3.622 1.00 0.00 > > ATOM 4 O GLY A 1 -23.652 -6.939 2.393 1.00 0.00 > > ATOM 5 H1 GLY A 1 -26.109 -7.957 4.035 1.00 0.00 > > ATOM 6 HA2 GLY A 1 -24.067 -7.811 5.488 1.00 0.00 > > ATOM 7 HA3 GLY A 1 -23.324 -8.902 4.328 1.00 0.00 > > ATOM 8 N SER A 2 -23.111 -5.869 4.298 1.00 0.00 > > > > pdb file obtaind from g_rmsf -f pr.xtc -s pr.tpr -n pr.ndx -oq > > command is as follws : > > > > ATOM 5 CA NGL 1 20.794 51.547 38.010 1.00 272.65 > > ATOM 12 CA SER 2 23.444 51.157 35.390 1.00 257.41 > > ATOM 23 CA SER 3 25.254 48.487 33.290 1.00 189.09 > > ATOM 34 CA GLY 4 28.474 47.777 31.510 1.00 114.27 > > ATOM 41 CA SER 5 27.814 48.657 27.860 1.00 195.51 > > ATOM 52 CA SER 6 31.164 48.167 26.020 1.00 217.99 > > ATOM 63 CA GLY 7 31.934 49.987 22.770 1.00 300.70 > > ATOM 70 CA LYP 8 32.204 48.057 19.510 1.00 248.64 > > > > so can I compare experimental B-factor with that calculated from MD? > > > > any help will highly appreciated. > I'm currently calculating b-factors too, and there may be two things > that you must think about. One is, as I understand it, that the b-factor > in x-ray scattering experiments is unaffected by motions in the > scattering directoion, effectively reducing the observerd mds of the > atoms so that B = pi^2 * 8 * msd_p, where msd_p is only the motions > perpendicular to the scattering direciton. Another thing to consider is > wether isotropic b-factors is suitable in your case. > > Erik
I don't think the scattering direction is a significant factor. Each atom occurs in multiple asymmetric units, and so in multiple orientations in the crystal, depending on the spacegroup. In any case, the diffraction intensities are averaged over multiple observations, taken at different crystal orientations with respect to the beam. More serious is that the B factor soaks up many sources of uncertainty: molecular motion (e.g. from crystal phonons), internal motions, static disorder, errors in the data, effects of partial occupancy, etc. In my experience, the rmsd calculated from a B factor is much larger than that calculated from MD, and quantitative comparison is impossible. But you may well be able to see qualitative similarities. Note also that you are comparing the molecule in solution with the molecule in the crystal, and there will certainly be differences near crystal contacts. There is no B factor for NMR structures. The closest equivalent is to look at the variation between MODELs in a PDB entry. Cheers Martyn -- *********************************************************************** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455 E-mail: martyn.w...@stfc.ac.uk * * Fax: +44 1925 603634 Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * *********************************************************************** -- 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/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/mailing_lists/users.php
