Hello. If you know the basis vectors for a crystal structure, you could write a script to convert them using matrix conversions like this en.wikipedia.org/wiki/Fractional_coordinates.
It depends on exactly what you want. So, this answer is very general. Load your pdb structure in VMD as the "top" structure. In TkConsole enter the following lines: set prot [atomselect top protein] $prot writepdb pdbfilename.pdb "pdbfilename" is the name of the protein file you want saved. This will save protein only (no water, no metals, no ions, no ATP, etc.)
+Moustapha Ahmed If you know which amino acids are the binding site, you simply read the pdb x, y, and z coordinates. These are the first three columns of decimal numbers. If you do not know the relevant amino acids, you will need to do experiments such as NMR or review the literature on your protein. I do not do docking studies. You will need to read the NAMD listserv and tutorials for that. Good luck!
Hello Sir, I would like to ask, how to generate data file for Lammps? I am using Materials studio to create the 3D models of some structures and save them as a PDB file. But I couldn't find any process to convert PDB file to data file. If you have any solution, please let me know. Thank you in advance.
Do you have the 3D coordinates of all of the atoms? If you put this into an .xyz format (columns = element x y z, e.g., C 1.1 0.2 5.0), you can load it into VMD and create a pdb file as shown one of my other videos.
hi
can you please tell me how to create PDB file from my NMR data?
I am not sure how to do this.
Can u please help how to convert the cartesian coordinates into fractional coordinates from a pdb file?
Hello. If you know the basis vectors for a crystal structure, you could write a script to convert them using matrix conversions like this en.wikipedia.org/wiki/Fractional_coordinates.
@@TroyMessina Thanks a ton 🙏 ❤
Hi..
I have calcium in my pdb file. How do i remove these calcium (metal) from my pdb file??
It depends on exactly what you want. So, this answer is very general. Load your pdb structure in VMD as the "top" structure.
In TkConsole enter the following lines:
set prot [atomselect top protein]
$prot writepdb pdbfilename.pdb
"pdbfilename" is the name of the protein file you want saved. This will save protein only (no water, no metals, no ions, no ATP, etc.)
i need to know how can i identify the coordinates of the ligand binding site from PDB file and how can i pick the atom for the docking procedure
+Moustapha Ahmed If you know which amino acids are the binding site, you simply read the pdb x, y, and z coordinates. These are the first three columns of decimal numbers. If you do not know the relevant amino acids, you will need to do experiments such as NMR or review the literature on your protein. I do not do docking studies. You will need to read the NAMD listserv and tutorials for that. Good luck!
+Troy Messina thanks for your replay :)
Is there any program that i could use in order to extract the network table from a pdb file?
I don't know of any program that does this specifically. Something like tcl scripts or Python might be able to be used.
@@TroyMessina thanks
@@RACEABLE No problem. If I come across something, I'll let you know. I've tried building connection tables from scratch. It's a pain.
How to parse the co-ordinates of atoms ?
I do not understand what you want to do.
Hello Sir, I would like to ask, how to generate data file for Lammps? I am using Materials studio to create the 3D models of some structures and save them as a PDB file. But I couldn't find any process to convert PDB file to data file. If you have any solution, please let me know. Thank you in advance.
I don't use Lammps or Materials studio. I am unable to help you.
can you pls give a tutorial on how to use a pdb editor? i can't open it after downloading.
ruclips.net/video/Xq9EHBJ80G8/видео.html
Thanks
hi i want to separate alpha carbon ,beta carbon ,oxygen and nitrogen and store different file separately
Try this video, and let me know if you still aren't sure. ruclips.net/video/55iZL0g7Se0/видео.html
Thanks for watching!
Why I can see only not readable text in every editor ?
What file are you trying to read? pdb and psf are text files.
OK, I want to edit *.pbd file not *.pdb, sorry, mistake
Hey bro nice video i need a help I want Protein name . Tyramine Receptor
Organism. Sitophilus oryzae rice weevil
In PDB format can u help me please
Do you have the 3D coordinates of all of the atoms? If you put this into an .xyz format (columns = element x y z, e.g., C 1.1 0.2 5.0), you can load it into VMD and create a pdb file as shown one of my other videos.
In hetatm file, what is Ibp
Can you post an example line from the file and provide more information? For what molecule is the file?