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Пікірлер
@almche8978 6 күн бұрын
مفيش شرح عربي
@adwaithmurali9097 9 күн бұрын
Students Hoping you make more videos of the same series
@sofiaruizhernandez5083 14 күн бұрын
Gracias! me ayudó mucho para mi tesis <3
@NITAMKUMAR 28 күн бұрын
i like your explainations .. very nice. thank you
@busemericacar36 Ай бұрын
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?
@Mohamedshehata 23 күн бұрын
writepdb file.pdb writepsf file.psf
@anisaaina4067 Ай бұрын
thank you? can we do this on our laptop?
@ghadakhedr7326 Ай бұрын
Gazakom Allah khairan
@ghadakhedr7326 Ай бұрын
Great 👍
@DarrellHolmes-q3u Ай бұрын
Moore Edward Allen Angela Lee Jennifer
@abdurrahmanusman6701 2 ай бұрын
It was the easiest, simplest, and most direct installation I have ever done on Linux. Thank you.
@mohamedsamy226 2 ай бұрын
How can i contact with you, Mohamed
@amneros 2 ай бұрын
Thank you for the very usefull tutorials. How do I specify the frames used for rmsf (like removing the highly variable start)?
@hassaanahmad3024 2 ай бұрын
Hello sir Whenever i run the code, vmd stops working What could be the reason?
@nazemrostami 2 ай бұрын
hello How do you calculate rdf in vmd for membrane and drug?
@zainab_sheikh 3 ай бұрын
THANK YOU!
@nenooo722 3 ай бұрын
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 ?
@lenon-dv9ko 3 ай бұрын
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
@lenon-dv9ko 3 ай бұрын
Hi, when I click create file, my VMD crashes and I do not see anything. Do you happen to know why this might be happening ?
@yaneve_t 4 ай бұрын
Very helpful, thank you so much
@magdymohammed114 5 ай бұрын
Please how can I continue an MD simulation that stopped due to electricity shortage
@aissaouisoumia9947 5 ай бұрын
how to do Radius of Gyration (RoG),
@Mohamedshehata 5 ай бұрын
there is already video in my channel about it
@HaifaAlMamari 5 ай бұрын
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 5 ай бұрын
you need to add TRF to your topology and parameters or maybe it is there but with difference name
@HaifaAlMamari 5 ай бұрын
@@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.
@HaifaAlMamari 5 ай бұрын
I was thinking in adding TRF, but I do not know how I can generated too. My current inputs files (gro, pdb and top) are form NanoModeler webserver.
@amkhalil256 5 ай бұрын
Thank you! May I get your email, Mohamed?
@amkhalil256 5 ай бұрын
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.
@Mohamedshehata 5 ай бұрын
Depends but you can start with VMD
@DrMubashirAziz_official 5 ай бұрын
Thankyou sir for considering my request and for a wonderful tutorial.
@DrMubashirAziz_official 5 ай бұрын
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 5 ай бұрын
Glad to hear that but it is getting busier day by day but I will do my best to add more
@DrMubashirAziz_official 5 ай бұрын
@@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
@ivangregoretti4554 5 ай бұрын
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.
@Mohamedshehata 5 ай бұрын
Yes, sure. I posted one to do it with the GUI but I may post a scripted one soon. Thanks Ivan for the suggestion!
@bnratha 6 ай бұрын
Can we make a homo-multimer or hetero-multimer of proteins in chimerax?
@biomedicalscientistmuhammad 6 ай бұрын
السلام عليكم دكتور محمد ، شكرا على المحتوى الرائع ده وارجو من حضرتك توضح لنا ، كباحث مش بفهم برمجة ومهتم بالمحاكاه والدوكنج ازاي اتغلب على المشكلة دي
@Mohamedshehata 5 ай бұрын
Start a project that needs you to understand and this will push you to learn.. good luck!
@kaushikkunte4266 6 ай бұрын
I have lammmps trajectory (.strj) file will it work?
@Mohamedshehata 5 ай бұрын
You can try to load it VMD, it can handle wide range of file extensions let me know if it can deal with .strj cos I don't remeber
@alwayslearning1282 6 ай бұрын
How can i get the graph of rg vs nanoseconds? Please help me in this regards. I'm a subscriber of your channel
@Mohamedshehata 5 ай бұрын
import your results to python and plot it with matplotlib ..chatgpt can help you do it easily
@HoseinTaghibigloo 6 ай бұрын
Dear Dr. Muhamed Shehata. I want to thank you and send my best regards for appreciating these applicable and valuable tutorials, you create on KZbin. 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.
@Md.Al-Amin-f9j 6 ай бұрын
Thanks
@Mohamedshehata 5 ай бұрын
Welcome
@Md.Al-Amin-f9j 6 ай бұрын
Thanks. Please, Upload a video on free energy calculation by VMD.
@Mohamedshehata 5 ай бұрын
Soon!!
@adeebafatimaceoaef 6 ай бұрын
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.
@toylemmons9320 7 ай бұрын
Great work here!
@Mohamedshehata 7 ай бұрын
Thank you!
@bobu5213 7 ай бұрын
Is there a way to also plot the (average) distance in A of the H-bonds along with this?
@abidullah8868 7 ай бұрын
hello sir, sir please make a video on how to calculate free volume by using vmd thank you sir
@yashikagirdhar 7 ай бұрын
sir how to remove ligand from protein?
@Mohamedshehata 5 ай бұрын
delete from the pdb file
@bonk747klm 7 ай бұрын
im new to vmd, where do i find the output filed of a solvate? i cant find them anywhere
@Mohamedshehata 7 ай бұрын
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
@bonk747klm 7 ай бұрын
@@Mohamedshehata ty, how can i generate a dcd file tho im using namd but im having some problems
@arunimachoudhury4709 8 ай бұрын
Please can you make a video about how to deal with patches between a metal center and ligand?
@TheMaxiking88 8 ай бұрын
How do you save a macromolecule + ligand as a combined pdb file? I can only save them separately..
@adeebafatimaceoaef 6 ай бұрын
same issue
@Mohamedshehata 5 ай бұрын
Chimera selectall then save pdb or vmd save all
@linaamin7235 8 ай бұрын
Thank u i managed all the steps but it is not running
@vanessagallegom 8 ай бұрын
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?
@wonderfullife5665 8 ай бұрын
thank you so much sir
@Mohamedshehata 5 ай бұрын
welcome!
@bijayantasircar2829 8 ай бұрын
Sir, how to calculate free energy using VMD?
@zineddinebenbekhti1203 9 ай бұрын
hello thank you for the explanation can you please add a video on how to build a gromacs files frome packmol output pdb file to run an md simulation ?
@amneros 9 ай бұрын
how to calculate the RMSD of a region of the protein, instead of the whole protein?
@Mohamedshehata 9 ай бұрын
you can modify your selection to for example: protein and resid 1 to 100
@habibiazka3078 9 ай бұрын
Halo Mohamed, when i wanna install mdtraj I found python error : The program can't start because api-ms-win-core-path-l1-1-0.dll is missing ...... Can you give me some solutions? thank you
@punctdan 9 ай бұрын
It's centered on protein but the box is constantly moving. How do I keep it in place when I'm recording it?
@Mohamedshehata 5 ай бұрын
align it to the first frame