[gmx-users] trjconv write frames to separate files
Hi, i'm trying to write each frame from the bebining time=0.0 to the end time=6000 to a separate file, but it writes only the 1frame at time 0.0: trjconv -f 1ktz_p1_em.gro -s 1ktz_p1_em.tpr -o 1ktz_0.pdb -b 0.0 -e 6000.0 -sep Reading frames from gro file 'GROningen MAchine for Chemical Simulation', 1148 atoms. Reading frame 0 time0.000 Precision of 1ktz_p1_em.gro is 0.001 (nm) Last frame 0 time0.000 i guess i should provide index.ndx of frames.ndx. i havn't found anithing about what to write in these files and in what format. Tania ___ 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] g_rms
Hi, i use g_rms to calculate rms, as reference structure (-s) i use myprotein.pdb file and trajectory (-f) is a trajectiry after MD MDprotein.pdb. The thing is that myprotein.pdb and MDprotein.pdb have the same atoms BUT their order within a residue is DIFFERENT. example: myprotein.pdb: ATOM 1 N ALA E 1 18.858 -22.883 26.306 1.00 0.00 ATOM 2 CA ALA E 1 19.106 -24.277 26.027 1.00 0.00 ATOM 3 C ALA E 1 20.206 -24.458 25.006 1.00 0.00 ATOM 4 O ALA E 1 20.156 -23.801 23.972 1.00 0.00 ATOM 5 CB ALA E 1 17.865 -24.819 25.301 1.00 0.00 MDprotein.pdb: ATOM 1 N ALA 1 18.861 24.179 26.290 1.00 0.00 ATOM 2 CA ALA 1 18.978 22.741 26.011 1.00 0.00 ATOM 3 CB ALA 1 17.670 22.190 25.440 1.00 0.00 ATOM 4 C ALA 1 20.069 22.592 24.949 1.00 0.00 ATOM 5 O ALA 1 20.120 23.450 24.070 1.00 0.00 whether g_rms work correct in this case? g_rms -s myprotein.pdb -f MDprotein.pdb ___ 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: Re: [gmx-users] rmsd on homologous protein structure
tahnk you i'll try that ___ 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] g_rms
Hi, i got strange results using g_rms. Does it by default uses mass weighting for superposition? I wrote my own script to calculate rmsd without mass weighting and it gives different results then using g_rms. If it uses mass weighting for superposition how not not use it? i tried select -mw no, but it doesn't work. namy thanks Tania ___ 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] rmsd on homologous protein structure
Hi, i want to calculate rmsd on homologous protein structures that have different residue numbers. As far as i understood g_rms gives only rmsd of the same structure in different configurations, but it doesn't fit homologous protein structures? In Option -f2 can i provide a trajectory of a homologous protein structure of it also have to be a reserence structure trajectory (which is provided in -s)? many many thanks Tatsiana ___ 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
