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 <mark.abra...@anu.edu.au> 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 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