After the process is completed, close the VMD Movie Generator window. Click on Make Movie and notice the progress. Please Log in or Create an account to join the conversation. Notice, the trajectory step is 1 and movie duration is 4 seconds now. Is it possible to upload density map to VMD together with the ref.tpr for the its visualization ? Where here might be source of the error? What are the best option for the visualization of density maps? E.g I have not found any of PDB files produced. Here ref.pdb consist of only protein atoms defined in groups 16 and 17 of new2.ndxĪt the same time If I chose group of receptor (17 in that case) from the same inputs - it produces normal density map. Reading frame 1800 time 708000.000 Segmentation fault a trajectory in VMD after removing the periodic boundary conditions. Making the movie After loading your files to VMD, press on a Window called VMD Main and press on Extension menu and select Visualization, and Movie Maker from the dropdown menu. Group 17 (Protein_&_!r_1-104) has 4117 elements I want to rotate a specific residue (say 'resid 7 and resname MET') by 180 degrees around x-axis and save the coordinates. Gmx densmap -f resp_complex_merged.xtc -s ref.pdb -n new2.ndx -od densmap.dat -wĪnd in that case obtained Segmentation fault error Rotation Movie Maker 1.0 - REQUIREMENTS: VMD Version 1.0. Open TkConsole and execute the following commands. Trjcat -f resp_complex_conf1.xtc resp_complex_conf2.xtc resp_complex_conf3.xtc resp_complex_conf4.xtc resp_complex_conf5.xtc resp_complex_conf6.xtc resp_complex_conf7.xtc -o resp_complex_merged.xtc -tu ps -catĢ- gmx densmap to calculate density plots of ligand defined in new2.ndx: You can also try the following: Load the trajectory in vmd and wait for all the frames. It's strange I have done all of those steps properly Key features of VMD include: General 3-D molecular visualization with extensive drawing and coloring methods and strong support for visualization of molecular dynamics Supports all major molecular data le formats, with no limits to structure or trajectory sizes except memory capacity and addressing Extensive atom selection syntax for choo.
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