Hello Mohamed, Thank you for your video. When I downloaded modeller on my mac it is a ".dmg" file which chimera states it doesn't recognize. Did you encounter this as well? I have to run the process locally since ChimeraX's website is still down for maintenance. I would appreciate any advice you can offer, thank you!
Hello, first of all, thank you for video. Moreover, how can i save this pro-asp pdb and psf files. Did you use "tk console" ? and how can i tk console for this work?
thank you. you really help me . i have made ab initio modeling for a peptide ( has not solvated structure) now i have its pdb but i can not generate psf file the problem starts when i choose guess and split chains option . there's a message of "couldn't find original pdb do yoy want to specify the location of the original coordinate file ?
when I click Create Chain, I receive this error message. ERROR: failed on segment MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over. ERROR: failed on segment MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over. while executing "segment $segid { pdb $segfile # We alias the C-terminal OXT atoms to OT2 so that psfgen has to guess one atom less. # Otherwise psf..." (procedure "psfsegments" line 37) invoked from within "psfsegments $logfileout" (procedure "::autopsf::afterchains_gui" line 66) invoked from within "::autopsf::afterchains_gui" invoked from within ".autopsf.chains.finish invoke" ("uplevel" body line 1) invoked from within "uplevel #0 [list $w invoke]" (procedure "tk::ButtonUp" line 24) invoked from within "tk::ButtonUp .autopsf.chains.finish" (command bound to event) Does anyone know what this could be? Thanks
thanks, i try this on my amber Pdb file and I got : "psfgen) unknown residue type TRF psfgen) extracted 60 residues from pdb file psfgen) setting patch for first residue to none psfgen) setting patch for last residue to none Info: generating structure... psfgen) unknown residue type AU Segmentation fault (core dumped)"
@@Mohamedshehata Thank you very much Mohammed for quick response. Actually, I am working on functionalized gold nanoparticle, I have the topology, pdb, and gro files. All these file has the same name of unrecognized atoms (AU, AUL, AUS(gold atoms), and GOL(peptide). I uploaded the top file in the toplogy files section and i delete the default files. I need to do this to get the charmm psf, so later on I can use Charmm-GUI multicomponent assembler to get MD inputs files. I am not sure if there is any other effective way to do that. I tried Parmed but it did not work.
Thank you, Mohamed for your tutorials! As a beginner in structural biology, do you recommend Pymol or Chimera? Also, I would appreciate if you can recommend some links for basics to help in structural biology.
Dr. your tutorial are very beneficial for begineers, i have started operating NAMD while watching your tutorial but your tutorials are decreasing day by day😂. Please make videos on regular basis. one please one request for next tutorial..please help to calculate free binding energies i.e. mmgbsa and mmpbsa using namd and please help to calculate PCA and pearson correlation through VMD
@@Mohamedshehata sir consider my request too i was able to thoroughly analyze RMSD trajectory through your valuable tutorials except MMGBSA and MMPBSA assays and PCA analysis. Please enlighten us with your expertise. anxiously waiting as my ph.d degree is on verge. please
Hi Mohamed. Thanks so much for the video. Short, sweet and packed with information. Could you point us to tcl scripts for making a movie like this one programmatically? Thank you.
Dear Dr. Muhamed Shehata. I want to thank you and send my best regards for appreciating these applicable and valuable tutorials, you create on RU-vid. I’ve found your videos as a guiding light of my journey to learn and practice molecular dynamics simulations. I would like to request a tutorial on dealing with big dcd files that exceed the memory limitations to analyze them for RMSD and RMSF. It would be great if asked tutorial to come after the last video because you’ve taught us here how to concatenate multiple dcd files, also it would be great for students who want to extend their knowledge to continue simulations and analyze them for longer timescales. If possible, covering different methods would be very helpful such as 1) using the bigdcd.tcl script within VMD, and 2. (( md.iterload )) from the MD-Traj as a memory-efficient way to analyze big trajectories in multiple directories. Thank you for your time and consideration. 🙏💐 Kind regards.
Thanks a bunch, sir, I was struggling hard in search of how to generate complex protein-ligand complex but couldn't find any entirely correct process to generate this file using the same Autodock tools but I came across this video accidentally and found the way! Thanks a lot again.
mostly in your installation directory if you use windows it will be in C program files/vmd. I recommend you change the working directory before you start so all the file be saved in the same folder. there is a video called scripting in vmd watch it to learn how to do this
Hi, it is the same procedure to complete a sequence? do you know any route that I can use to complete the sequence in Chimera and save it as a new PDB?
