Re: [gmx-users] B-factor to large? Input for TLS
Hi Mark, Thanks for your reply. I will check if the reference structure and the trajectory fit. Cheers Henrey On Mon, Nov 7, 2011 at 9:15 PM, Mark Abraham wrote: > On 5/11/2011 11:05 AM, Henri Mone wrote: >> >> Dear Gromacs Users and Experts, >> >> I want to calculate from my xtc trajectory the B-factor and the >> anisotropic temperature factor. I'm using following gromacs command: >> >> $ g_rmsf -f traj.xtc -o rmsf.xvg -oq bfac.pdb -ox bfac2.pdb -s >> structure.pdb > > Does this reference structure in -s make sense for the trajectory supplied > for -f? If the computed atomic deviations make no sense, then neither will > the fluctuations. I have no idea if g_rmsf takes proper account of > periodicity, but you might need either to massage the trajectory suitably > with trjconv (see website for suggested workflows), or supply a .tpr with > the correct box information. > >> I want to input the resulting PDB file to the "TLS" Server [1] to >> calculate the hinge residues for my system. >> The B-factor which "g_rmsf" is calculating seem to be to large, they >> are in the range of 2000 to 6000 (last column without the "1.00" >> prefix) [2]. >> The website [3] suggests that a reasonable B-factor should is in the >> range of 21 to 200. Also the TLS server [1] complains that the >> b-factors are in the wrong range. I did several test but I have no >> idea what I"m doing wrong. The trajectory is with 250ns long enough to >> get for my small system a convergence on the B-factor. >> - I thought it could be a unit problem, what are the B-factor units >> which "g_rmsf" uses? Could this cause such an huge difference in the >> b-factor? > > g_rmsf converts to Angstroms before writing B-factor output to PDB, as you > would expect. > > Mark > >> - What is the standard unit for the b-factor in the PDB definition >> (from the PDB database)? >> - What is a realistic range for the b-factor? >> - What else could be the error source, what am I doing wrong? >> >> >> Thanks, any help is welcome, >> Henrey >> >> ---1: TLSMD SERVER >> http://skuld.bmsc.washington.edu/~tlsmd/ >> >> >> >> ---2: bfac2.pdb : >> ... >> ATOM 6146 N GLY 435 97.841 52.072 37.712 1.006712.85 >> ATOM 6147 HN GLY 435 97.972 52.020 37.437 1.006676.79 >> ATOM 6148 CA GLY 435 97.953 52.003 37.883 1.006739.30 >> ATOM 6149 HA1 GLY 435 97.975 51.822 37.563 1.006956.61 >> ATOM 6150 HA2 GLY 435 97.554 52.041 37.972 1.007042.78 >> ATOM 6151 C GLY 435 98.601 52.111 38.350 1.006210.20 >> ATOM 6152 O GLY 435 98.552 51.909 38.905 1.006278.92 >> ATOM 6153 N ASN 436 99.235 52.437 38.127 1.005772.75 >> ATOM 6154 HN ASN 436 99.262 52.602 37.668 1.005803.67 >> ATOM 6155 CA ASN 436 99.904 52.574 38.508 1.005343.12 >> ATOM 6156 HA ASN 436 99.947 52.400 38.918 1.005671.18 >> ATOM 6157 CB ASN 436 100.537 52.527 37.948 1.005355.63 >> ATOM 6158 HB1 ASN 436 100.960 52.556 38.127 1.005098.00 >> ATOM 6159 HB2 ASN 436 100.553 52.657 37.601 1.005272.78 >> ATOM 6160 CG ASN 436 100.587 52.258 37.586 1.006031.62 >> ATOM 6161 OD1 ASN 436 100.582 52.138 37.675 1.006435.18 >> ATOM 6162 ND2 ASN 436 100.641 52.163 37.176 1.006306.09 >> ATOM 6163 1HD2 ASN 436 100.689 51.993 36.928 1.006834.63 >> ATOM 6164 2HD2 ASN 436 100.652 52.264 37.117 1.006062.64 >> ATOM 6165 C ASN 436 99.947 53.023 38.917 1.004590.56 >> ATOM 6166 O ASN 436 99.651 53.240 38.597 1.004290.70 >> ... >> >> ---3: B-factor range at 3 Å resolution >> http://www.p212121.com/2009/04/12/b-factor-range-3-resolution/ -- gmx-users mailing listgmx-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
Re: [gmx-users] B-factor to large? Input for TLS
On 5/11/2011 11:05 AM, Henri Mone wrote: Dear Gromacs Users and Experts, I want to calculate from my xtc trajectory the B-factor and the anisotropic temperature factor. I'm using following gromacs command: $ g_rmsf -f traj.xtc -o rmsf.xvg -oq bfac.pdb -ox bfac2.pdb -s structure.pdb Does this reference structure in -s make sense for the trajectory supplied for -f? If the computed atomic deviations make no sense, then neither will the fluctuations. I have no idea if g_rmsf takes proper account of periodicity, but you might need either to massage the trajectory suitably with trjconv (see website for suggested workflows), or supply a .tpr with the correct box information. I want to input the resulting PDB file to the "TLS" Server [1] to calculate the hinge residues for my system. The B-factor which "g_rmsf" is calculating seem to be to large, they are in the range of 2000 to 6000 (last column without the "1.00" prefix) [2]. The website [3] suggests that a reasonable B-factor should is in the range of 21 to 200. Also the TLS server [1] complains that the b-factors are in the wrong range. I did several test but I have no idea what I"m doing wrong. The trajectory is with 250ns long enough to get for my small system a convergence on the B-factor. - I thought it could be a unit problem, what are the B-factor units which "g_rmsf" uses? Could this cause such an huge difference in the b-factor? g_rmsf converts to Angstroms before writing B-factor output to PDB, as you would expect. Mark - What is the standard unit for the b-factor in the PDB definition (from the PDB database)? - What is a realistic range for the b-factor? - What else could be the error source, what am I doing wrong? Thanks, any help is welcome, Henrey ---1: TLSMD SERVER http://skuld.bmsc.washington.edu/~tlsmd/ ---2: bfac2.pdb : ... ATOM 6146 N GLY 435 97.841 52.072 37.712 1.006712.85 ATOM 6147 HN GLY 435 97.972 52.020 37.437 1.006676.79 ATOM 6148 CA GLY 435 97.953 52.003 37.883 1.006739.30 ATOM 6149 HA1 GLY 435 97.975 51.822 37.563 1.006956.61 ATOM 6150 HA2 GLY 435 97.554 52.041 37.972 1.007042.78 ATOM 6151 C GLY 435 98.601 52.111 38.350 1.006210.20 ATOM 6152 O GLY 435 98.552 51.909 38.905 1.006278.92 ATOM 6153 N ASN 436 99.235 52.437 38.127 1.005772.75 ATOM 6154 HN ASN 436 99.262 52.602 37.668 1.005803.67 ATOM 6155 CA ASN 436 99.904 52.574 38.508 1.005343.12 ATOM 6156 HA ASN 436 99.947 52.400 38.918 1.005671.18 ATOM 6157 CB ASN 436 100.537 52.527 37.948 1.005355.63 ATOM 6158 HB1 ASN 436 100.960 52.556 38.127 1.005098.00 ATOM 6159 HB2 ASN 436 100.553 52.657 37.601 1.005272.78 ATOM 6160 CG ASN 436 100.587 52.258 37.586 1.006031.62 ATOM 6161 OD1 ASN 436 100.582 52.138 37.675 1.006435.18 ATOM 6162 ND2 ASN 436 100.641 52.163 37.176 1.006306.09 ATOM 6163 1HD2 ASN 436 100.689 51.993 36.928 1.006834.63 ATOM 6164 2HD2 ASN 436 100.652 52.264 37.117 1.006062.64 ATOM 6165 C ASN 436 99.947 53.023 38.917 1.004590.56 ATOM 6166 O ASN 436 99.651 53.240 38.597 1.004290.70 ... ---3: B-factor range at 3 Å resolution http://www.p212121.com/2009/04/12/b-factor-range-3-resolution/ -- gmx-users mailing listgmx-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
Re: [gmx-users] B-factor
- Original Message - From: Tsjerk Wassenaar Date: Friday, July 2, 2010 14:10 Subject: Re: [gmx-users] B-factor To: Discussion list for GROMACS users > Hi, > > >> ATOM 12 CA SER 2 23.444 51.157 35.390 1.00257.41 > > > > The last column is the occupancy (1.00) and temperature factor > numbers> concatenated. You can fix the symptoms by editing the > file by hand so that > > these numbers occupy the right columns - see the PDB format. > > > > This illustrates buggy behaviour from GROMACS. > src/tools/gmx_rmsf.c probably > > needs to call set_pdb_wide_format(TRUE) before > write_sto_conf_indexed().> Please file a bugzilla (see GROMACS > webpage).> > > I disagree. The PDB file is fixed width, and the format for the > b-factor field is %6.2f. This means that the above line is a proper > PDB ATOM definition. Using the Gromacs pdb_wide_format generates > a PDB > file that may not be compatible with other programs. I would argue True. I misread what was happening with the pdbform variable and leapt to a conclusion. The observed GROMACS behaviour now looks correct. I don't recall what symptoms the OP had, but presumably they were related to the function of the correctly-formatted file with some (other) software that assumes space-delimited PDB fields. Mark > though that Gromacs should at least warn when trying to write numbers > larger than 999.99 to the b-factor/occupancy field. > > Cheers, > > Tsjerk > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > Groningen Institute for Biomolecular Research and Biotechnology > University of Groningen > The Netherlands > -- > gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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
Re: [gmx-users] B-factor
Hi, >> ATOM 12 CA SER 2 23.444 51.157 35.390 1.00257.41 > > The last column is the occupancy (1.00) and temperature factor numbers > concatenated. You can fix the symptoms by editing the file by hand so that > these numbers occupy the right columns - see the PDB format. > > This illustrates buggy behaviour from GROMACS. src/tools/gmx_rmsf.c probably > needs to call set_pdb_wide_format(TRUE) before write_sto_conf_indexed(). > Please file a bugzilla (see GROMACS webpage). > I disagree. The PDB file is fixed width, and the format for the b-factor field is %6.2f. This means that the above line is a proper PDB ATOM definition. Using the Gromacs pdb_wide_format generates a PDB file that may not be compatible with other programs. I would argue though that Gromacs should at least warn when trying to write numbers larger than 999.99 to the b-factor/occupancy field. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing listgmx-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
Re: [gmx-users] b-factor
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 603455E-mail: martyn.w...@stfc.ac.uk* * Fax: +44 1925 603634Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * *** -- gmx-users mailing listgmx-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
Re: [gmx-users] b-factor
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 -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-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
Re: [gmx-users] B-factor
- Original Message - From: shahab shariati Date: Tuesday, June 29, 2010 15:51 Subject: [gmx-users] B-factor To: gmx-users@gromacs.org > Dear Erik Marklund > thanks for your attention > > I saw www.pdb.org. there is b-factor in pdb > files being in this website but pdb file obtained form g_rmsf -f pr.xtc > -s pr.tpr -n pr.ndx -oq command, has not B-factor. > > my bfac.pdb > file is as follows : > TITLE Protein in water > REMARK THIS IS A SIMULATION BOX > CRYST1 62.008 62.008 62.008 90.00 90.00 90.00 P 1 1 > MODEL 1 > ATOM 5 CA NGL 1 20.794 51.547 38.010 1.00272.65 > ATOM 12 CA SER 2 23.444 51.157 35.390 1.00257.41 The last column is the occupancy (1.00) and temperature factor numbers concatenated. You can fix the symptoms by editing the file by hand so that these numbers occupy the right columns - see the PDB format. This illustrates buggy behaviour from GROMACS. src/tools/gmx_rmsf.c probably needs to call set_pdb_wide_format(TRUE) before write_sto_conf_indexed(). Please file a bugzilla (see GROMACS webpage). Mark > ATOM 23 CA SER 3 25.254 48.487 33.290 1.00189.09 > ATOM 34 CA GLY 4 28.474 47.777 31.510 1.00114.27 > ATOM 41 CA SER 5 27.814 48.657 27.860 1.00195.51 > ATOM 52 CA SER 6 31.164 48.167 26.020 1.00217.99 > ATOM 63 CA GLY 7 31.934 49.987 22.770 1.00300.70 > ATOM 70 CA LYP 8 32.204 48.057 19.510 1.00248.64 > ATOM 92 CA GLY 9 35.314 45.957 18.630 1.00184.40 > ATOM 99 CA GLY 10 37.064 42.607 19.150 1.00139.99 > ATOM 106 CA GLN 11 37.224 39.007 17.810 1.00106.39 > ATOM 123 CA VAL 12 34.754 36.657 19.540 1.00 78.29 > ATOM 139 CA ARG 13 33.244 33.847 17.550 1.00 79.41 > ATOM 163 CA PHE 14 32.044 30.277 17.980 1.00 23.96 > ATOM 183 CA SER 15 30.254 27.737 15.740 1.00 44.68 > ATOM 194 CA ASN 16 26.794 26.277 16.430 1.00 54.17 > ATOM 208 CA ASP 17 28.154 23.097 18.090 1.00 52.38 > ATOM 220 CA GLN 18 30.914 24.937 19.880 1.00 25.27 > ATOM 237 CA THR 19 28.404 27.377 21.340 1.00 24.72 > ATOM 251 CA ILE 20 26.264 24.487 22.620 1.00 35.92 > ATOM 270 CA GLU 21 29.004 22.497 24.430 1.00 22.96 > ATOM 285 CA LEU 22 30.324 25.797 25.950 1.00 13.17 > ATOM 304 CA GLU 23 26.874 26.467 27.560 1.00 26.01 > ATOM 319 CA LYP 24 26.474 22.877 28.710 1.00 37.38 > ATOM 341 CA LYP 25 29.944 22.657 30.270 1.00 29.72 > ATOM 363 CA PHE 26 29.484 26.037 32.040 1.00 33.01 > ATOM 383 CA GLU 27 26.304 24.837 33.730 1.00 56.55 > ATOM 398 CA THR 28 28.194 21.907 35.400 1.00 71.22 > ATOM 412 CA GLN 29 31.264 24.057 36.290 1.00 61.11 > ATOM 429 CA LYP 30 31.314 27.927 35.980 1.00 53.89 > ATOM 451 CA TYR 31 35.124 27.747 35.600 1.00 54.07 > ATOM 472 CA LEU 32 37.594 25.107 34.310 1.00 52.72 > ATOM 491 CA SER 33 40.974 24.187 35.600 1.00 49.43 > ATOM 510 CA PRO 34 43.864 24.147 33.110 1.00 41.67 > ATOM 524 CA PRO 35 44.074 20.337 32.590 1.00 46.11 > ATOM 530 CA GLU 36 40.404 20.317 31.650 1.00 30.32 > ATOM 545 CA ARG 37 40.464 23.597 29.640 1.00 17.05 > ATOM 569 CA LYP 38 43.434 22.497 27.460 1.00 19.61 > ATOM 591 CA ARG 39 41.524 19.337 26.310 1.00 21.22 > ATOM 615 CA LEU 40 38.184 21.167 25.940 1.00 10.93 > ATOM 634 CA ALA 41 39.834 23.657 23.510 1.00 10.81 > ATOM 644 CA LYP 42 41.344 20.617 21.670 1.00 20.84 > ATOM 666 CA MET 43 38.004 18.787 21.490 1.00 19.62 > ATOM 683 CA LEU 44 35.884 21.877 20.620 1.00 16.95 > ATOM 702 CA GLN 45 38.504 23.247 18.140 1.00 23.14 > ATOM 719 CA LEU 46 38.814 26.507 20.170 1.00 17.31 > ATOM 738 CA SER 47 41.784 28.247 21.770 1.00 22.52 > ATOM 749 CA GLU 48 42.464 28.237 25.540 1.00 18.67 > ATOM 764 CA ARG 49 41.984 32.017 25.510 1.00 22.59 > ATOM 788 CA GLN 50 38.484 31.627 24.050 1.00 17.42 > ATOM 805 CA VAL 51 37.614 28.917 26.620 1.00 8.87 > ATOM 821 CA LYP 52 38.664 31.067 29.630 1.00 15.01 > ATOM 843 CA THR 53 37.104 34.267 28.220 1.00 21.29 > ATOM 857 CA TRP 54 33.794 32.697 27.320 1.00 15.97 > ATOM 881 CA PHE 55 33.164 31.167 30.720 1.00 16.56 > ATOM 901 CA GLN 56 34.244 34.267 32.580 1.00 27.30 > ATOM 918 CA ASN 57 31.854 36.577 30.640 1.00 31.82 > ATOM 932 CA ARG 58 29.204 33.887 30.940 1.00 28.78 > ATOM 956 CA ARG 59 29.414 34.027 34.740 1.00 42.57 > ATOM 980 CA ALA 60 28.834 37.777 34.520 1.00 52.64 > ATOM 990 CA LYP 61 25.674 36.957 32.590 1.00 47.32 > ATOM 1012 CA TRP 62 24.714 34.207 35.090 1.00109.93 > ATOM 1036 CA ARG 63 25.094 36.337 38.210 1.00145.64 > ATOM 1060 CA ARG 64 22.154 38.367 36.850 1.00409.17 > ATOM 1084 CA SER 65 19.994 35.337 36.560 1.00567.55 > ATOM 1095 CA GLY 66 20.044 34.427 40.200 1.00313.57 > ATOM 1110 CA PRO 67 22.124 34.867 43.420 1.00232.72 > ATOM 1116 CA SER 68 22.484 31.017 43.640 1.00296.77 > ATOM 1127 CA SER 69 26.064 29.747 43.910 1.00746.26 > ATOM 1138 CA CGL 70 26.794 26.717 41.750 1.001312.96 > TER > ENDMDL > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/searc
Re: [gmx-users] B-factor
shahab shariati skrev: Dear *Erik Marklund* what do you meant from See the reference for the pdb file format? is b-factor a file? please guide me more. I am beginner in gromacs. Hi, A pdb file can store many things other than atomic coordinates, for instance b-factors. The pdb-format is not a gromacs invention however, and its documentation for the pdb-format can be found at www.pdb.org -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-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
Re: [gmx-users] B-factor
shahab shariati skrev: Hi all excuse me for my past incomplete email. I want to calculate B-factor using g_rmsf command as follows: g_rmsf -f pr.xtc -s pr.tpr -n pr.ndx -oq this command give me a pdb file whereas I want to obtain text file (numeral value of B-factor ). how to obtain B-factor value from this pdb file? any help will highly appreciated. Look in the b-factor field. See the reference for the pdb file format. -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-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
Re: [gmx-users] B factor and R factor
Hi Lu, These are respectively a parameter refined in crystallographic structures and a quality measure of such structures. The B factor (or ADP -> Atomic Displacement Parameters) give you an idea of the thermal motion of the atoms. The R factor is a measure of the agreement between the experimental data and the refined model. I hope this helps. Cheers, Miguel 2008/4/2, shuai lu <[EMAIL PROTECTED]>: > > Hi, > >What do B factor and R factor mean ? And what can be indicated fome > them? > > -- > Lu Shuai > > > ___ > gmx-users mailing listgmx-users@gromacs.org > 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 > -- http://www.pangea.org/mol/spip.php?rubrique2 ~~~ Je suis de la mauvaise herbe, Braves gens, braves gens, Je pousse en liberté Dans les jardins mal fréquentés! Georges Brassens ___ gmx-users mailing listgmx-users@gromacs.org 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
Re: [gmx-users] b-factor
tangxuan wrote: Dear all, I have got a pdb file by command g_rmsf and option -oq, and the content of the file is like this: Could you tell me which column should be the b-factor? Google is your friend :-) Try "pdb file format" 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? If you want to know what GROMACS does in detail, that's why the authors gave you the source code. There might be a literature source there, but I think this is more like textbook material, e.g. google "definition crystallographic b-factor" Mark ___ gmx-users mailing listgmx-users@gromacs.org 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
Re: [gmx-users] b-factor
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 > REMARKTHIS IS A SIMULATION BOX > CRYST1 148.918 148.918 148.428 59.89 59.89 90.00 P 1 1 > MODEL1 > 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 listgmx-users@gromacs.org > 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 listgmx-users@gromacs.org 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
Re: [gmx-users] b-factor
On Oct 22, 2007, at 10:07, tangxuan wrote: 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 REMARKTHIS IS A SIMULATION BOX CRYST1 148.918 148.918 148.428 59.89 59.89 90.00 P 1 1 MODEL1 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? It is the last column that contains the B-factor value. 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? Usually the B-factor can be viewed as an incertitude factor (between 0-100). I'm not sure about the implementation in g_rmsf, but unless anyone else here on the list corrects me, I think you could assume this is what g_rmsf writes. Thank you! Tang Jiaowei ___ gmx-users mailing listgmx-users@gromacs.org 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 ___ gmx-users mailing listgmx-users@gromacs.org 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
Re: [gmx-users] B-factor calculations
Jon Ellis wrote: Hello users I am using B-factors to look at protein flexibility, using g_rmsf. I have a 3-ns simulation of an RNA strand bound to a 30-mer peptide. I did g_rmsf on the complex using the -oq option to obtain the bfac.pdb file, which gives me the B-factors averaged over the entire trajectory (I think). Is it reasonable and physically valid to calculate b-factors varying over time, say by computing g_rmsf for smaller segments of my trajectory? If so, what would be a reasonable time interval for the averaging? In principle yes, but 3 ns is not a lot. You may want to try different analyses like essential dynamics, and prolong your trajectory. Thanks in advance for your help Cheers Jon Jon Ellis PhD Candidate, Thompson Group Institute of Biomaterials and Biomedical Engineering/Dept of Chemistry University of Toronto Lash Miller 147 (416) 978-6568 [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
